So is there any way of getting around this when it wants the tracks to have a certain length?
There are always ways around those things. The question is, is it worth the time and effort.
No.
...
There are 2 paths someone could take to fix it.
The first would be to change the calls to use track number. Of course, that requires hunting down all the audio triggers, and changing the calls. Then making sure the area for reading the TOC is available. Etc.
The second would be to build an iso image with the audio in place, and using the offsets in the new image for the calls. Of course, you would have to do that every time you changed the track lengths.
Can it be done? Yes. Would it be easy? Not unless you know a -lot- about both the game and the cd layout.