I found a way that works, even if it's not pretty at all: Merging layers then creating a new mask of the resulting layer. I had to remove the old islands manually - not a big deal for my purposes, but I missed a small corner on the western coast. Totally avoidable had the layer masks worked properly. Overall this is a big, big big minus in the Painter 12 evaluation.

Here are my notes on tectonics:

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And this is the latest WIP after I tried to apply some of those thoughts to the image:

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The horizontal line is again an Inkscape bug of some sort. I honestly never thought I'd use any graphics program to an extent where I hit weird and obscure errors...