If your source imagery has data all the way up to the boundary, then it should work just fine. Geoconvert doesn't care if the source images are split across multiple source files, just so long as all of it is there.
But, as an example--if you have two source images that don't quite meet (maybe for some reason there is a 100m gap between the photo data), then a mask file will be created, if masks are enabled. If they aren't enabled, it will skip generating that tile since it doesn't have complete imagery to produce it.
Likewise, if your source imagery ends halfway across a tile, and masks are enabled, geoconvert will create a mask file to let the lower levels show through where your source imagery ends, and you'll still end up with half a tile of orthophoto imagery which displays correctly in the sim.
The orthophoto masks are actually very simple: they are just an extra hidden image layer that tells a converted orthophoto tile where it needs to be transparent. If you're familiar with using alpha channels for transparency in computer graphics, they work a lot like that.
They become confusing because there is so much else going on that it's hard to keep track of all of it (source imagery resolution aka zoom level, geoconvert levels, and the fact that it's not immediately obvious which level you're currently viewing when flying in the sim at various altitudes). And if you've built a bunch of scenery that generated masks, those masks will force any newly-generated scenery of the same level to still be transparent in the same places unless the masks are removed. That can become a very tedious process, so that's why some of us started suggesting that everyone avoids creating mask files altogether.
If you already have scenery that was converted with masks enabled and those masks were produced, it means you have some tiles that only had partial image coverage. If those masks then get deleted without removing their corresponding image tiles as well, that's when you'll start seeing the black areas, because there is no data there and the lower levels can't show through it without the mask.