The "sleeve" should sit solid on the strut perch. the coil should fit solid to the perches on the sleeve. That lip you speak of should not interfere unless you are actually speaking of the strut perch. It's harder to explain than I thought...
Basically the only thing you should need to modify for a correct fit is the either the strut mount (unlikely) or the bump stop (cut it in half). If we had a visual example I could explain better.
What kind of coil-overs?
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