I think there's some confusion here. The OP is talking about the bedding compound used to install the skylight? Others are talking about what they're using to seal the skylight once installed? I don't think anyone is wrong, it's just confusing as all get out to read.
I used the butyl as well when I did ours. It appeared to me that was what was used on the original install? No doubt the hardest part of the job was prepping the roof - getting all the old gook off it.
1997 37' HR Endeavor, 275hp Cat, Freightliner
03 CR-V Blue Ox, Ready Brake