What you need is a Flue Flashing.
That fibrous roofing stuff is not heat proof, so you need to make as much clearance between the flue and the sheets as possible.
If the flue is a single skin type you need a high temperature flashing.
You can get them from building supply places or heating specialists.
Cut the centre hole to the diameter of the flue and slip it down from the top of the flue until it touches the roof. Mark out the edge of the skirt on the roof and cut the roofing back to about 50mm inside the mark. Cover the overlap area with high-temp silicone, and screw the skirt down onto it at regular intervals with sheet screws.The skirt is very flexible and will conform to the corrugations. Make sure you get it right down into the "valleys" though, and in good contact with the sealant. Particularly on the "uphill" side.
If you make sure the centre hole is a good stretch-fit over the flue you wont need to seal it there.
I would really recommend you put a weather cowl on top of the flue too. Keeps the rain from mixing with the smoke residues and rotting the flue from the inside.
According to the building regs a heating appliance flue should extend above the apex of the roof. If it doesn't you might get wind swirling the fumes back to ground level nearby. If your shop is not part of a habitable building, you can ignore the regs, but it's up to you to decide if the fumes might be a nuisance.