We use the PVL system in my son's KTM65. Most PVL kits are similar? On the KTM kit, the new flywheel/rotor is NOT keyed. You need to put a dial-gauge in the spark plug hole to find exactly TDC.
Now say you want to time for 0 TDC. Install flywheel so that 0 degree index on flywheel (the new PVL one) is exactly even with 0 degrees on the new stator (while dial gauge is reading perfect TDC).
You want x degrees before TDC. A normal question, but NOT a normal answer here. I guess because they figure we now have a dial gauge involved, the suggested timings are given in mm. I think they are saying to roll back on the crank so that the dial gauge drops x mm, then install the new flywheel so it's alignment marks match the stator. PVL seems to give its timings in mm BTC. NOT degrees BTC.
See:
http://www.pro-flo.com/images/PVL Instructions (Back).JPG
We got our PVL from pro-flo, and they seem to be very knowledgeable. Their website has as much about these ignitions as I have found.
For a 250cc the installation instructions say: Analog systems 1.8-2.2mm; Digital systems 0.8-1.0 mm.