My two bits:
It's perfectly fine, and I have done it. The only thing you need to realize is that unique mods (that only work on one, not the other) cannot be used on the other, for obvious reasons. For example, the megaglest packed with MG has particle tags that are not yet usable in GAE, thus, you cannot use that version of the Megapack in GAE (though you can download a vanilla glest version from the
MDC, and a future version of GAE should be able to support these extra particle tags). Likewise, GAE only mods such as military cannot be used on MegaGlest because they contain code that only GAE can understand.
I do believe that GAE only lists GBM maps from the map folder (can't be 100%, but very sure), so the maps combine fine, as only MG will read the MGM files.
GAE and MegaGlest use separate folders for scenarios and data (such as language files), so they should be good.
So to answer your question, they can be combined fine.
Of course, as Wciow pointed out, its always a good idea to have a multiplayer install separate (this can be MegaGlest, GAE, or Vanilla Glest), though it needs to be completely unmodified (ie: cannot change the tech trees). Ideally, this version will have the latest versions of most mods (unmodified, cannot stress that enough) and its recommended to download the Omega Map Pack (now version 2, secretly updated with GG v5) to get 60+ of the most recent maps available. MegaGlest may be best for multiplayer, though having both Vanilla and GAE available too is a good choice, since both still have working multiplayer (abet, needing you to enter the IP addresses).
