My very first motorized bike was built back in 2007...I think. Or early 2008. I drilled the down tube to mount the front of the engine on that bike because I basically didn't know better and that's what the kit said to do.
I finally retired that bike this spring, frame still intact. It was an aluminum frame too, built on an Electra Coaster 7.
That said, I always regretted the decision to drill the frame and wish I hadn't. I never drilled a frame again in the six or seven builds I've done since then. And part of the reason I retired the Electra was because I'd drilled the frame.
Now again, in this case it never showed any signs of cracking or weakness, but I still think it's a bad idea.