It will be fine, when you get the flywheel resurfaced they'll machine down the entire face, so the larger disk will engage evenly across the surface of the flywheel.
Most people that install the WRX clutch don't have this issue, but if there were enough wear to allow for a difference in hight on the clamping surface you'd have the problems you've experienced.
I installed a Exedy WRX clutch on my Legacy and it's been running that way for over 40k miles. I made sure to get the flywheel resurfaced and I never had a problem.
Strange. There's been a WRX clutch bolted to a (non-resurfaced) Legacy Turbo flywheel in my car for many thousands of miles as well. Even if the disc was the tiniest bit larger than the friction surface (which I don't remember being the case) the clutch should still operate normally. Do you know what condition your flywheel was when the clutch was installed?
For the record, yes you could re-machine your flywheel for a slightly larger friction surface if need be.
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the flywheel i remember it just had normal wear. not blue hot spots or anything. I didnt even noticed any raised lip beyond the 8-7/8" contact area.. but i think it might be kinda concave shaped so its grabbing a bit on the 1/8" edges.
its a comp 6 puck clutch so it has a lot more bite.
