So I recently started NV with the mod, "Tale of two Wastelands", allowing me to play F3 in the NV engine as well as playing both with the same character. I'm using the GoG FNV and the Steam F3.

Achievement gain is somewhat sporadic. I failed to get those for level 10 and 20. Then, apparently, 11 days ago I got the one for scouting Zion but not for arriving in Zion - I haven't actually been to zion in the gog version but have finished it on Steam.

I know absolutely nothing about achievements, but suppose, the answer is in the cited sentence somewhere.

I don't see how; the most recent one i received is a random one from one dlc which i haven't touched on gog and I have all the dlc achievements on steam, not just one.