I have tried almost the same thing - the only way that works would be to add the script to the scripts menu and launch it using mcr from there. Basically it works but as soon as the menu changes the mcr stops working (or would launch a wrong script).
(The adding to script menu tags are stored in powerlogic.ini, so that's another file to manage, as you mention)
We are now up to 5 files to manage, but it does work...
You can start a Script at program startup this way as well:
Edit the "Target" line of the shortcut used to start Logic, to read something like this:
C:\MentorGraphics\9.0PADS\SDD_HOME\Programs\powerlogic.exe /s"C:\PADS Projects\Scripts\MyScript.BAS"
I use this method to run a script for Layout, but never actually tied it for Logic.