There are quite a few people that I know running them under a stock cover - no problem. They do stretch so you will be replacing it in time - 80 to 100 thousand miles with proper maintenance.
I just put a double roller set on my recent rebuild and it fit under the cover with no clearance issues.
on what application did you use a gear drive? *If you did not like that little squeek....you will not want to run a gear drive. I could have easily gotten a gear drive for mine, but a little research told me it was not what I would want! Put you a good double roller on there and be done with it.
The gear drives are known for their special sound - but you could always hide it with a blower...... Tere are loud and quiet gear drives but the quiet ones are not really quiet - just not as noisy.
I have never had a problem with my double rollers including having them fit under stock timing covers. The Pete Jackson Gear Drive on the truck sounds wicked though! But gear drives are exspensive. If you own a SBF then summit makes a nice gear drive for a fair price and they can be had for a good price on ebay too. Its all your style. Just dont fall for the "Noisy" and "Quiet" crap. There is no quiet gear drive. Atkeast not that I have heard