mdomer,
For you issue with Stratus overwriting items changed in CAD, have you tried playing with the Admin > Settings > Specific to AutoCAD > Assembly Conflict Resolution? This might work with Packages, too. In the event of a conflict, the setting allows you to pick if Stratus is always right, AutoCAD is always right, or if the user should be prompted.
As for the LISP, yes that should be achievable. You could also use a * wildcard with the code above. if you wanted to find package 123-456-789, I believe you can search for *789.