I've been stage managing for a company that uses two AEA Guest Artist contracts on every show. I'm a non-AEA stage manager. They don't go to three Equity, because the third contract is supposed to be the stage manager.
I'm mostly going to second much of what has already been said. I agree that you will get different answers from AEA when you call with questions on Guest Artist, depending on who you are asking. I find that many of the employees there don't seem to know much about Guest Artist contracts. The rulebook and the contract itself are your best assets.
The primary areas where I have run into issues are with video-taping and recording, as these issues are not detailed in the contract. I default to the most restrictive assumptions and get written permission for archival video in advance. The rest of the issues that I usually face are very company specific, namely the length of the contract (which for us is two weeks shorter than the rehearsal period for the non-equity cast), and reimbursement for personal costume items. Basically, directors who want equity actors in before their contract has started, and producers who don't want to pay for nylons, tights or shoes. In both cases, being clear and persistant with the contract requirements usually works fine.
Oh and per diem. In my area, per diem and the definition of "out of town" is very loose, so those rates are negotiated individually. It's a done deal by the time it's in my hands, but I often get questions from auditioning AEA folks, and there isn't a clear answer I can give them, because AEA doesn't lay out requirements for specific per diem amounts in the GA contract.