Your BBS rep is covering his and his company's ass by saying that. They would have been sued a thousand times over at this point by "enthusiasts" who take their wheels to some slack jaw to powdercoat and bake them at 1000°F for 10 hours (both numbers exaggerated to illustrate a point, which would weaken the metal especially in the extreme case I listed).
That said, the website listed below gives you an idea of heat treatment for aluminum alloys. The situation that you're worried about most closely resembles precipitation heat treatment or "artificial aging" (which actually has the ability to strengthen some properties of metal, but I'm not getting into that). Have a look at table 4, at the prescribed temperatures and times at which they are treated. This is only for the listed types of aluminum alloys but gives you a general idea.
As a practicing engineer, those that design things use a safety factor and I have to believe that BBS is part of that category. I don't know how you use your car or even what wheels you're considering powdercoating, but I'm willing to bet that you aren't going to get close to even 50% of the failure point designed into your wheel (assuming it's a legit wheel manufacturer)
I had my wheels powdercoated without a second thought, and would do it again.
I'm not getting into a discussion about molecular structure.
Sorry to get off topic, I'm done.
Anyone going to Cars & Coffee at the Music Factory tomorrow?