About the mts with aac-latm, switching to FFmpeg Safe Mode for audio encoding is the better workaround. With FFmpeg Safe Mode the audio delay is ignored, and for this capture is the right thing. Somehow MediaInfo is exposing a wrong delay.
I have found that remuxing the mts to mkv has some benefits: the filesize decreases a lot (padding within the mts?) and FFMS2 is now able to decode the 2nd aac track. In this case, major drawback, the audio delay is messed up even more. Again, FFmpeg Safe Mode with the remuxed mkv works as well.
Still to test the mts with e-ac3
Bye