MBtiles seem convenient and portable, and I have successfully imported them to Manifold 9.
How did you import MBtiles into 9? That's not a format directly supported by Manifold. If you import .png, there's no need to build intermediate levels, so that might be a result of whatever process was used to import mbtiles. For example, GDAL might not build intermediate levels.
However, when MBtiles are first loaded into Manifold 9, they generate an error (little red stop sign on the map tab, message in the message console) - "Image cannot be rendered because it stores no data for intermediate levels"
That's not an error in the data, that's an advisory message the image import is not yet complete, in that the image is not ready for use. Native Manifold dataports do all that for you, but the presumption is if you use a third party import (GDAL) you don't want Manifold in any way altering what that third party you called upon does for you.
1) Is there a better workflow for clearing the errors on the MBtiles?
Yes, there is. The "Messages" part of the User Interface topic puts it better than I can, so I'll just copy it:
If we double-click open a component and a red message icon appears in the window's lower tab, we should choose View - Messages from the main menu to read the message. Blank drawings showing a message icon usually indicate lack of a spatial index, which Manifold will offer to build for us. Blank images showing a message icon usually indicate a need to build or update an index or intermediate levels, which Manifold will offer to do for us.
F7 is a keyboard shortcut for View - Messages (as the View menu tells us).
Once you build intermediate levels, you never have to re-do it, as then the image is fully provisioned and ready to go. Reprojecting the image will, as a side effect of reprojection, also build intermediate levels. But it's not the right way if all you want to do is provide intermediate levels. Much better to simply click View - Messages and then click the button to have Manifold build intermediate levels
Given that not everyone reads the Basics topics, and also given that for those who do it's easy to skip over various details, I think it would be good if one could click on the icon and see the message without needing to call up View - Messages. I get it that doing that complicates with extra code where the icon can go (interfering with normal click commands on tabs, for example) but it would be nice to have. I've sent in a suggestion to that effect.
The other way to have better workflow, of course, is to import as .png. That's way more portable than MBtiles.
In terms of sharing, share projected images using TIFF format, which Manifold writes as GeoTIFF. GeoTIFF embeds projection info, and I believe that Arc can read GeoTIFF, perhaps even without requiring the user to spend a few thousand on an extension product. :-)
As to how to ensure your images have the correct projection, that depends on whatever information is provided from the original source of the images. If it provides enough information to display the image with correct georeferencing in Google Earth, no doubt there's a way of extracting that information in a way that it can be used in GIS.
If you're lucky, it could be you could use the kml overlay file provided, as shown in the Example: Import KML with GroundOverlay Image example topic.