Part of doing repair work is learning how to work, where to keep your tools, how to set your bench up, etc. so that you never, never damage the valuable personal property of others.
We at times do ghost building for other Luthiers where we are shipped a neck, and box from a pro finisher and then we do the final assembly. Mind you the instrument has already been buffed to a high shine when we get it. We have to set the neck angle and attach, fret the things, make and install nuts and glue on the bridge and make a saddle and do the final set-up.
Again the instrument is highly polished and the finish is perfect.
It's very rare for us to ever damage anything although it does and can happen from time to time but when it does you fix it and being a Luthier means that you have the chops to fix what you do too.
Most of all though what I wanted to add is that after all of the handling and final assembly it's pretty much standard fare to take the completed instrument to the buffer and buff it out one final time so that it's perfect in every way (beyond maybe how it was built..).
So two take-aways for you J. First is that folks work on finished AND valuable instruments every day. We worked on a $75,000 archtop yesterday with the client present..... and one need not damage anything with a little thought to your work flow, bench layout, and I'll add using tools and vices.... that won't damage anything.
The other take-away is that it's pretty much expected that after final assembly the thing could benefit from taking it to the buffer one final time but be careful, buffers like to throw brand new guitars right across the room....
dang things....PS: No effort is made to encapsulate the thing in protective coverings although we do use a protective shield that the guys who are coming to our fretting class will use and receive too.
PSS: If working on a finished instrument makes you nervous I was that way too but you get over it with time and experience and a track record of doing no harm helps too.
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It also taught me to use whatever simple precautions are available. That's why I was wondering if people here have hit on any protective measures that help to prevent damage such as particular materials between the guitar and the bench top or masks over the top and back, etc., that I may not have thought of or be unaware of. 