Changing a fleet configuration or a base configuration doesn't make it a custom object. It's the objects that are made from scratch and not included in the TE that are custom....
I'm going to try to do these from memory since I've misplaced the MA Map guidelines I had.
1) There must be 3 countries with equal resources.
2) No custom objects. (textures are OK, buildings, runways, etc. are not)
3) No airfields over 5k
4) Towns must be within 5 miles of base
5) A full, working strat system must be in place for each zone. (roads, tracks, barges)
6) Roads, tracks must be no longer than 10 miles.
7) No embedded skins. (which I don't think you can do anymore anyway)
8) All source files are to be sent when you submit the map. Not just the .res file.
I could have sworn there were 10 key points, so if I missed anything someone please fill in the gaps.
And I know there are maps out there with exceptions to these rules, such as towns being more than 5 miles from a base. So, I don't think there is anything etched in stone. If it's reasonably playable I think the rules bend.