Oh - I see the advanced section in the OP somewhat addresses this with a custom MWGIDMap tag. This does (somewhat) imply that other mods that deal with schematics either their own tags or do not address this issue at all.
i.e. it would be dangerous to use schematics made by (for example) Schematica with this mod if they contain mod blocks...
MWG tries to be as compatible as it can. When saving a schematic, it uses the block IDs of the current world, and if it tries to load one without an MWGIDMap tag, it uses the current world ID mapping back. So, if a schematic is partly broken or if it's loaded with another program, it will at least work with the same world. I don't know how other mods handle this.
There are no dimension restrictions. You can use the biome whitelists and blacklists for each schematic for this purpose. By default, schematics are saved with the Nether and End biomes blacklisted, and this is the also the case for most of the included structures.