The last time I was consolidating "best of" from different performances (from a stage musical), I put different performances on different layers. Yes, there were timing differences, but then I would just split/keep across all tracks and slide one layer to match another after dropping out parts that I didn't want. There was at least one time when I had to pull a very short segment of a single track from one performance to another. Surprisingly, I got away with it.
I found keeping all tracks separated for editing and then mixing afterwards had some benefits. Sometimes I needed to edit different tracks at different points or with different softedge slopes to make the cleanest overall edit. This worked especially well where the edit was during applause.
It can be a bit of a PITA editing this way, but it gives the best chance of the best overall result, IMO.
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