If the correct BPM for the audio is 120, then that is what you should set it to in OctaChainer, regardless of the length of the file. The tool then knows how long each step is and can therefore place slicepoints correctly.
When you set the BPM, the sample length in number of bars is automatically adjusted to match this (to, say, 4.25), both in the tool and on the OT. So with time stretch on nothing should change. But iirc I round off number of bars to the same accuracy as what is shown in the display on the OT. I haven't checked if setting the BPM on the OT actually sets a more exact bar length and just display a rounded value. So if you set the BPM on files that aren't a precise number of bars in length and something doesn't sound quite right with timestretching on I'd try to set the BPM again on the Octatrack afterwards. You might get a more accurate bar length that way.
The .OT file is not a text file, unfortunately. There is a link to the OctaChainer source code in the first post of this thread. Look in otwriter.h and otwriter.cpp for details on what the .OT files contain.