the soft synth is not an audio track, it's capturing midi controller data - note played, parameter tweaked etc.
why not create another track set to audio and have that source as the output from the synth?
you hit record and both tracks record - one records the midi and the audio track records the output of the synth.
you can add a bus and capture the bus pre effects even to capture raw audio for mixing later on.
if there is midi data that is not captured and the soft synth is manually tweaked but not recorded then the audio and the midi will not sync cause now the audio track has captured audio of live performance but the midi does not have this data. could cause some problems later on if you moved things around or had to change up something - not a huge biggy but the two tracks will not be exact.
I'm not sure I understand the problem though as the program will do sort of what you are asking to be done. I think.