Pretty cool indeed!. My initial thoughts are to frame the roof (perhaps octagonally?) around the trunk to give a more or less constant gap, then make up a gaiter out of some tarpaulin type material e.g. plastic coated textile. I'd clamp the top cuff around the tree using a long length of stainless steel worm drive banding - basically an oversized jubilee clip. I'd lap the bottom cuff and fasten down onto the roof covering with suitable clamping strips.
It would be a giant version of the leather gaiters that can be fitted over the swivel housings of a Landrover axle. Imagine a flat shape rolled into a truncated cone. The ends are joined together with a double overlap seam. On the Landrover gaiters, they are simply laced together with bootlace!
Hmm, nice idea as it may be to have a tree in your workshop, I would avoid it if at all possible for the following reasons:
Tree trunks are rarely smooth and making a watertight seal is going to be a real pipper. Even if you manage it with the use of mastic etc the tree grows each year, meaning any seal will not be stable over time.
Trees grow. Imagine how much over say 5-10 years. Not only do you have the increase in girth, you also have branches above that will drop wet leaves onto your roof each year, causing a damp problem at least unless you get up and clean them off regularly.
Space. We all want more space in our workshops. I know I couldnt work round a tree trunk in mine! Even if its in a corner or agaist an edge imagine all the wall space you will lose just to be able to say 'yeah, but it looks cool!'
Roots. You will either have to have your shop on piles/stilts or risk damaging the roots to lay a concrete/slab pad to site your shop on. Roots also break the surface in time, especially near the trunk. Not much help for getting a stable level floor.
Your post may have been a tounge in cheek job to which I have posted a serious reply (wouldnt be the first time I have got the wrong end of the stick :roll: ) but I would seriously avoid it if possible. Build a tree seat round it as your first project and sit and admire you workshop from it with a beer :wink: