Luckily I haven't run into that, but then I'm not using any commercial software currently and the stuff in the official repositories tends to work the way you would expect it to. Generally your settings should work pretty much independently of any program you happen to be running - xkb in particular is processing the key events at quite a low level.

Regarding the line editing tools you mentioned that sounds to me like something built in to the native UI toolkit (I'm just guessing here though). Reconfiguring how physical keys are interpreted can obviously only do so much. I'd never heard of those shortcuts before and they sound like a really useful feature.