WM did use Penn. Station in Baltimore. I just checked my March 1954 Official Guide and there were still a few passenger trains running and they stopped at Penn. Station after leaving Hillen Street. I am not up on Baltimore, but I wound up with a stack of the PRR Technical & Historical group's magazines (up in attic and I'm not going there tonight). I seem to remember that about 15 - 20 years back, there were several issues devoted to Baltimore from pre-PRR days to the Amtrak era including coverage of the construction and history of Penn. Station in Baltimore.
My dad once made mention of a Western Maryland platform at Penn, which was on the opposite side of the station (the JFX side) from where the tracks are today. There was an odd, blocked off (with railings) staircase which I remember seeing as a kid - the area has since been walled off from the rest of the main floor - that, he said, led down to that platform.
I asked around about WM tickets at Penn Sta and nobody, me included, can remember for sure. But we all agreed that in the later years at least, it would not have been cost effective for the WM to have a ticket window in Penn Sta. There was a ticket agency at the nearby WM Hillen Street station. Hard to tell what the arrangement was in its hayday. More than likely any WM ticket sold at a PRR ticket window would be done for a commission to the PRR.(Just a guess)
For the most part, the passengers were commuters and had commutation tickets (weekly, monthly) that they could purchase at the other end of their trip. Passengers could also purchase a cash fare on board from the Conductor. Passengers coming from and going to the PRR could have a interline ticket for transportation on both the WM and PRR.
So I think you can rest assured that a WM ticket window in Penn Station was unlikely.
The sad part is that the ticket agent at Hillen Street just died recently and he would have known for sure.