Yesterday I ran into this very same issue I think. I was videoing and taking pics our local fire station (working with the fire chief's blessing) and things were going great. I had them pull the trucks out and got some good pictures. Then, near the end, I wanted to do a fly though of one of the bays so I asked them to move all but one of the trucks back into the station. This is the type of station that has doors on each end of the garage so they can drive the trucks straight through them and is maybe 75' across. I knew that it was likely that I would lose GPS but I had hoped that it wouldn't be fast enough to be a problem. I got maybe 10' in and the PS2+ starts to slew to the right. I try to correct it, and then it suddenly shoots forward very quickly, getting a little too close to one of the trucks. I bring it back to the center and immediately bring it to the ground but I came in fast and it tipped over and did the crab walk for about another 10' before I could power down. I didn't have the nerve to try again, and while i was disappointed that I didn't get the video I wanted things worked out well over all.
I doubt that your location would be as much of a Faraday cage as a metal fire station but you should be careful. I like the idea of trying to do a walk through with the phantom and wished that I had tried that yesterday!
And, yes, I am scaredy 'fraid of manual mode and won't be trying the fly through again in that mode. :?