When Union Station was built (opened c.1906 as I recall), low-level platforms were the standard -- e.g., Broad St. Station (no 30th St. then), Jersey City, Wilmington (1903?), Baltimore (1911), etc. (North Phila. got high-level platforms when the track grade was raised, but didn't have them originally.) High level platforms were installed in Washington, as you say, when the Metroliner project was started and were confined strictly to tracks used by the Metroliners and other NEC trains.
Traditionally, specific track areas were assigned to B&O, PRR, and the southern lines -- B&O at the west side, PRR in the center, and, of course, southern lines on the low-level tracks at the east end. There were overlaps, especially in high-traffic periods, but generally each road had its own assigned tracks. PRR trains did use the lower level tracks when necessary for whatever reason, but I don't recall any B&O trains doing so.
The old B&O-PRR separation pretty much continues to this day, withMARC Camden and Brunswick-Martinsburg trains using the westerly tracks.
