Pleaserefrain from blaming users.
Nobody is blaming users. Referring inaccurately to the order of channels in data causes errors when people work with software that can rearrange channel to output assignments using multiband data, and it also causes errors in programming, SQL, and so on. Avoiding errors matters to everyone. Referring inaccurately to the order of channels in data also contributes to the mountain of totally wrong advice on Internet.
The USDA paper is a good example of that: it is simply wrong when it says that in NAIP four band data the first band is red, the second green and the third blue. Why does USDA make that error? Most likely because somebody looked at the "RGB" nickname and cluelessly assumed that the data channels in the data also appeared in R, G, B order.
That is an error, a blunder similar to ones made all the time when beginners hear "Latitude / Longitude" so they assume that the latitude number comes first in coordinate pairs.
There's nothing wrong with saying "Hey, it's OK to use the nickname 'RGB' to refer to images that use three color outputs. Just don't assume that the nickname literally specifies the data order, which might be RGBA, ARBG, BGR, ABGR, BGRA, etc." That's what Manifold does.
If you look at running text in the Manifold documentation, RGB images are simply called RGB images, just like they are everywhere. Nobody's pushing uphill against the accepted name. If you look at how Manifold works, it takes what somebody calls an "RGB" .tif and it correctly assigns the right channels to red, green and blue outputs, even though the actual data channel ordering is BGR. Works great. There's none of this "oh... you called it an RGB? Are you sure you don't mean BGR? well then I'll do it backwards..."
When you have a system that works with specific channel ordering in very many different formats and which allows users to specify which output will be driven by which channel, you cannot escape referring to the actual channel ordering. You can't just use the term "RGB" all the time, because the channel ordering is not always RGB. In fact, it's usually BGR. Referring to the actual channel ordering using a term like BGR is more compact than something like "channel ordering where data acquired in blue wavelengths is in the first band, data acquired....".
Photoshop and very many other consumer graphics editors don't need to get into any of that because they don't provide facilities to pick and choose and re-assign channels from manychannel formats into four outputs.
Photoshop users don't actually work with the specific data channels within a wide variety of different formats. Instead, once you import an image into Photoshop the "channels" are identified as Red, Green and Blue. That's because Photoshop decides how to assign data channels from the original file to R, G and B outputs and thereafter doesn't use any naming or channel ordering as it was in the original file. Instead, they refer only to the outputs by the color name. In Photoshop, every three band image is an "RGB" image because that is what Photoshop names the channels it uses.
Photoshop doesn't allow channel reassignments like Manifold does. There's none of this "first channel," "second channel," and so on stuff, assigned as you see fit to some desired color output. That's because Photoshop isn't either a GIS or a remote sensing image manipulation package. If you want to reassign channels to outputs, it is a much harder process in Photoshop than in Manifold.
Here is a video (watch it expanded to full screen, so you can read the small text in the video) that shows how it is done in Photoshop, using a four band NAIP .tif: https://vimeo.com/188925635
Like it or not, your multiband .tif image gets imported into what Photoshop forever more will call Red, Green, Blue, and Alpha channels. If you don't like what Photoshop did by default, you have only one recourse, a manual process that is shown in that video: you first must split your image into four grayscale images, each one of which is named with "Red," "Green," "Blue," or "Alpha" as part of the name by the splitting tool. You then use another tool to create a new RGB image that takes data for that image's Red, Blue, and Green "channels" from the various grayscale ones.
That can lead to a lot of confusion. For example, suppose the TIF you imported into Photoshop was one of the rare ones that actually uses RGB ordering for data channels and not BGR ordering. Photoshop will import it wrong, because the channel that Photoshop imports into what Photoshop calls the "Blue" channel will actually be Red data. You can fix that by splitting the image into "Red", "Blue" and "Green" grayscale images and then creating a new Photoshop RGB image where you take the "Blue" grayscale and put that into the image's "Red" channel.
Photoshop also misuses the name "Alpha" when dealing with four-band data like NAIP. "Alpha" universally means transparency, but not in Photoshop in the case of NAIP.
Fire up your copy of Photoshop and import into it a four band NAIP. By default, the Alpha channel is turned off in Photoshop's channels dialog. That's a strange thing to do, since usually Alpha is an important part of per-pixel transparency. But in this case, it's turned off.
You can see what happens in the video, where accidentally the commentator turns on the Alpha channel for a moment. What happens? The image goes red. If you try it yourself in Photoshop on your own desktop, you'll see that when Photoshop imports the data from the fourth NAIP channel it treats it as some sort of Red override. If you turn on just Blue and Alpha you get red colors. If the channel is what Photoshop calls it, Alpha, but it is treated as a color channel and not transparency, well that's just plain wrong. If you think it is OK that Photoshop takes a name like "Alpha" that universally is used to mean "transparency" and instead uses it as a Color output, well, I respectfully disagree. I think that's confusing, especially for beginners. If "Alpha" means transparency, use it for that.
The erroneous USDA PDF is not unique, by the way. It's amazing how much disinformation there is out there on the web. One reason I chose that video, for example, is because it was created by a University Geography Deparment and yet it provides bad info: He says to create an "infrared image" by using the fourth, Alpha Photoshop channel as the new Red channel, but to keep using the Green grayscale for the Green channel and the Blue grayscale for the Blue channel.
But that's wrong if you look at what the traditional Color Infrared (CIR) assignments are, where the near-Infrared channel drives the Red output, the Red channel drives the Green output, and the Green channel drives the Blue output.
Personally, I think the new topic on creating CIR from NAIP says it better: there are various assignments that can use the near-Infrared band in four band NAIP imagery to create a false color image, but the traditional assignment used to create what are called Color Infrared (CIR) images is the given one, which happens to match the result way back in the day when Kodak CIR film was used to photograph in the same bands.