There shouldn't be an issue with merging mapping changes in general, because it would be very difficult for you to interfere with one map while working on a different one (see reasons below). It's just difficult to know when there would be conflicts if you're doing script/event editing and expand/move the memory location of events.
Reasons plus mapping info: if you make changes that don't fit the allocated memory block AdvanceMap just doesn't save. It doesn't give an error, though, so you have to quit and reload the ROM to know for sure, which then means you lost changes unless you exported the map first. So basically, when you put in a lot of time in a map EXPORT IT AS WELL, don't just save. You can always fiddle with it to reduce the size in memory or load it into a block in a different place if all else fails. I'm not sure how to go about fully deleting maps to free up blocks (it's incredibly messy since I think you have to cut all of the maps after the one you're deleting, delete the map, then paste all of the other maps back), so it's probably best to avoid too much saving-in-a-different-location cases at this point.
@Johuotar: No specific reason why to make mons learn moves at interesting levels, other than to keep it interesting. Like you mentioned, though, this makes it so that mons that learn moves every 5 levels are pretty unique and gives them some flavor of their own. Generally, though, I only remember legendaries learning moves every 5 levels (and it always seemed like a cop out/laziness because they had already leveled past the vast majority of the moves anyway), just as a note.