If your powdercoater hasn't started your frame yet, tell him to wait.
Some aluminum frames have a post-welding heat treatment that the heat of powdercoating can somewhat undo, leading to a significant-but-unknowable loss of strength and durability. I know that Cannondale frames are not supposed to be powdercoated for exactly this reason, and Klein may well have the same restrictions. It certainly wouldn't surprise me.
It's also entirely possible that the differences are mostly theoretical, and Cannondale put that warning out as a CYA. Plus, a '91 Klein MTB frame isn't as scary-thin as the later Trek ones, let alone 'Dale's CAAD frames.
That said, I wouldn't do it. A head tube weld failure while honking at speed would be ugly. I pulled a stem out on a BMX bike once... the crash happened so fast that I missed it. (The event, not the ground. That, I hit.)
--Shannon