A few more answers-
:01 and :59 shows and truncating record requests - no way to record less than the scheduled time today. In the case of the :01 overlap, this should only impact you if you are tuner constrained at the overlap time. If this is the case, you can setup a manual recording for the non overlap time to record the show. I know, it's not ideal but with two tuners this will hopefully mitigate. Another option is to see if one of the shows airs at an alternate time. Some of the ABC shows re-run on Saturday night. The final option is to manually stop the earlier recording early/start the other one later (ie you manually tell the box to stop 2 minutes before the scheduled end time).
Truncating recorded shows - sorry, this is not currently supported due to reasons outside of MSTV control.
Bypassing MPEG encoder on analog channels - not currently supported and beyond MSTV control.
New/Re-run show handling - as you might imagine, we're at the mercy of the EPG data (and the networks reporting to the EPG data companies). If we record one and the guide data has enough information for us to determine that the others are duplicates, the others will not record.
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