I do not know of any Gimp forum equivalent to those old Some-Subject For Dummies books. There is Reddit but in my opinion for some reason you get lots of really poor advice, - don't use Gimp - use AI - etc.
Your post is a bit over long try and trim it down to the bare essentials, however I think your problem is when you CTRL-V for a paste you get a new layer and that might get exported as a separate page in the edited PDF. The solution there is merge the new layer down.
You can get Gimp 3 to use a floating layer much the same as Gimp 2.10 it is Edit -> Paste As -> Paste As Floating Data
There is no shortcut for that but you can make your own.
For what it is worth an example video (4 minutes) First minute is Gimp 2.10 to compare with Gimp 3
https://sendvid.com/n4mwdavx
Your post is a bit over long try and trim it down to the bare essentials, however I think your problem is when you CTRL-V for a paste you get a new layer and that might get exported as a separate page in the edited PDF. The solution there is merge the new layer down.
You can get Gimp 3 to use a floating layer much the same as Gimp 2.10 it is Edit -> Paste As -> Paste As Floating Data
There is no shortcut for that but you can make your own.
For what it is worth an example video (4 minutes) First minute is Gimp 2.10 to compare with Gimp 3
https://sendvid.com/n4mwdavx