It just seems to me that that it is a bit odd that when you designate a source for the target layer, all the currently loaded control points get wiped out.
Casual language that doesn't capture what's going on may be what makes it seem odd.
Target windows don't have control points of their own, although in casual language it is natural to refer to it that way.
By default, every window starts as a source window. With source windows you can mark control points at various locations in that source window, using whatever the coordinate system for that source window happens to be. Source windows have control points with specific names.
What changes a source window into a target window is when you tell that window to get control points from some other source window. That's what the drop down box at the top of the register pane does.
Target windows don't have control points of their own. They become a target window by declaring their role is guiding the georegistration of the specified source window by using the control points that source window defines.
To use the drone photo example, when in the Register pane for the Map Target window you choose EV-001 as the source window, you're telling the Map Target window to take the list of control points it uses from the EV-001 window.
When you click into different spots in the Map Target window, you're not creating a control point. Instead, you're marking what location in the Map Target window is supposed to correspond to the context control point that is defined in the EV-001 window and is picked by the table cursor in the Register pane list shown for the target window.
All of the control points in the list shown by the Register pane for the Map Target window are defined in the EV-001 window. If you want to add a control point or to delete a control point, you have to do that in the EV-001 window, not in the Map Target window.
Suppose you started with the map window that you planned on using as a target window, but while it was still a source window you created 100 control points at the locations of various cities. Those control points don't have any correspondence to some other source window that you want to georegister. If you like, you can save those control points as a drawing.
That's basically using the Register pane as a shortcut way to create a drawing full of points that have default names like those used by default for control points. When you create control points in a source window and then save those control points to a new drawing, that's what you are doing. You could do the same thing by just creating a drawing layer in a map and adding points to it. But then you'd have to name each point individually. Using the Register pane to do that is just a shortcut.
Suppose you now want to use that source window as a target window to guide the georegistration of some other source window. The first thing you do is tell it to use the control points from the desired source window. That's an explicit instruction saying, "throw out any control points I've created, because now I want to use control points from some other window."
When you "create control points in the target window first" you're not really doing that, since target windows don't have control points. You're just using a source window (which is what the target window is until you tell it to take control points from some other source window) as a short cut way to create a drawing of points with default names.
If you then create control points in the source window you want to georegister, and then tell the target window to use those control points to georegister that source window, if you created the control points in the source window following the pattern (the mutually visible features) of the control points that were saved, well, you can then save yourself the time of manually marking locations in the target window by importing the corresponding locations from the points drawing you created and saved eariler.
That isn't going to add control points to the target window, either. It will just scan the names used in the saved control point drawing that is being used, and when any of those names match the control points being brought in from the source window, it will use the coordinates from the saved control point drawing for those names as the locations to use for georeferencing the corresponding control points.
The whole relationship between source and target windows when it comes to georegistration is very simple and clear, but it does require grasping that key nuance that target windows don't have control points of their own, because being a target window means it is working with a list of control points from the source window that is to be georeferenced. Get your head around that one, simple idea and all the rest falls into place very simply.
But explaining that to folks who have a different mental model, one of independent sets of control points, one set for source windows and one set for target windows, takes a lot of words, as you can see above. I think that's why Manifold's documentation explains it the way it does, in a simpler way that allows people to recycle familiar concepts even if they are slightly off.
Let me close with one thing: I think it's a way more typical situation that you'd start with the source component to be georegistered, because that's the thing that has to get done. You have to use whatever are distinctive features in that source component. It doesn't matter if there are other features that are clearly visible in the proposed target, if those features aren't visible in the source component.
I'd therefore respectfully suggest that perhaps the workflow that starts by marking control points in the source as the primary activity, and then only as those points are marked moves on to marking corresponding locations in the target, is probably easier both to do and to teach than first marking locations in the target.