GIMP's layer system is definitely unique, sadly it hasn't much in common with the selection tool. In that sense, yes, it is unintuitive when migrating from other apps. I'd argue it's not that complicated, as gimp even highlights the buttons you should be pressing like a mobile game, but it is a complete non sequitur so back on topic...

If you use "select all" in any program to cancel selections, I don't know what to tell you. Like ok, GIMP is the jankiest of em all if you do that, no contest, but the rest doesn't behave correctly either if your expectation is that it'll work just like it did before you did any selecting. The flashing selection line around the whole page should be a pretty strong indicator of something being different.

Honestly, many GUI program, doesn't even have to be a raster art program; vector art like illustrator, 3D modeling like maya, some music programs, our custom spreadsheet stuff at work, even many file explorers, as far as I remember they all have the ctrl-shift-a shortcut and all would behave quite differently if you used ctrl-a excepting the same result. I'm genuinely at a loss where you'd get the idea to use ctrl-a to cancel a selection. Like I understand the intuition you proposed, but at what point do you just forget everything else you ever did on your computer?