Quartus TCL API in ModelSim or vice versa

I don't know that this has even been done, but you can always give it a try.

I could tell you that you can probably figure out a way to use Tcl itself to establish a connection between the two EXEs, and use that to transfer Tcl commands, but you are better off finding another solution.

For example, simply partition your script into two, and have one script make a system call to call the other EXE on the portion of the script.