There have been several previous discussions on the forum regarding the advisibility of waiting to install the engine before fitting the cowls. Even though the scribe marks are accurate it only takes a small deviation at the fuselage junction to move the spinner end an ugly amount. The plans and the factory say that you should just cut the cowls to the scrib lines before having the spinner back plate installed for reference. But several of the early builders had difficulties getting good spinner clearance and based on this experience, I waited to have the engine installed to fit the cowl. There is really no reason to install it early unless you like to gamble.
Here are a couple of pictures, the first one is my final spinner clearance of slightly more than 1/8":
This may be unfair, but here is a picture, of the factory demo plane:

I don't know, but assume the factory demo cowl was fitted in plan sequence.
I think the plans should be changed on this, it is much easier to do the job after the engine is mounted, and will result in better clearances and eliminate redos which entail drilling out a lot of rivets and building fiberglass repairs.
As far as engine vibration in the mounts, the Rotax is pretty smooth especially with a dynamic balance done. I doubt if vibration of the engine in the mounts would be an issue if the spinner clearance were even less than 1/8", but 1/8" looks good and gives a bit of room for installing and removing the cowls.
Tony