You're correct about the reason. To compensate for the BFrame alignment shift (which surprisingly is fairly regular after each commercial cut), I've introduced a parameter in Expert Settings called Subtitle segment offset, the purpose of that is to shift the subtitles by a predetermined amount , incrementally (not just once initially) after EACH commercial segment cut. By default it's set to 3.2 (by my tests) but you can play with that to get the right number for yourself (+ve or -ve).
For your second question, unfortunately the remuxing process is DEEPLY integrated into MCEBuddy with various checks and balances using ffmpeg so it really can't be swapped for handbrake.
However, you can run handbrake prior to MCEBuddy picking up the file using a batch script and then dropping the converted file to mcebuddy monitor directory to pick it up.
BTW, instead of handbrake, you can use ffmpeg to burn in teh subtitles also, you can customize the FFMPEGBackUpRemux section in mcebuddy.conf to include the additional settings reuqired to burn in the subtitles.
See this page for more details:
https://trac.ffmpeg.org/wiki/How%20to%20burn%20subtitles%20into%20the%20video
For your second question, unfortunately the remuxing process is DEEPLY integrated into MCEBuddy with various checks and balances using ffmpeg so it really can't be swapped for handbrake.
However, you can run handbrake prior to MCEBuddy picking up the file using a batch script and then dropping the converted file to mcebuddy monitor directory to pick it up.
BTW, instead of handbrake, you can use ffmpeg to burn in teh subtitles also, you can customize the FFMPEGBackUpRemux section in mcebuddy.conf to include the additional settings reuqired to burn in the subtitles.
See this page for more details:
https://trac.ffmpeg.org/wiki/How%20to%20burn%20subtitles%20into%20the%20video