I don't see a way to make the location or department fields mandatory on the Manage Intercompany Sales Orders screen, so I'm considering some kind of browser automation to correct this, which is probably not the best idea. Is there a better way to make sure that intercompany SOs generate with these values. I'm guessing I could transform them automatically from the IC PO.

UE can be a friend, but imo if you have requirements like defaulting values, dynamic filters, probably best build your own "Manage Intercompany Sales Orders' as a Suitelet I guess to NS's defense this can get a bit complicated as the location/department can be subsidiary specific and they might not be shared between the two subsidiary? You'll have to expand on your use case but I'm pretty sure customization is required