Well, JAR-OPS 1 allowance for 90 and 180 deg. line-up (which is what your perf. manual should comply with) does indeed seem to assume you line up behind the taxi line. This problem is worse at some airports than others, some don't seem to have the problem at all.
So the answer would be: yes, turn-around allowance is included in all calcualtions and - on limiting runways - should be the overriding factor in where you do your line-up (physical edge clearance + safety margins for outboard wheel & wingtip still respected, of course).
Brgds,
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