Some history info, including historic photos, in this WSDOT paper: [
www.wsdot.wa.gov]
Most of the bypass is former NP Prairie line - see the link/map above. A portion near the Freighthouse Square station is former Milwaukee. There was no connection between the two (in that area) until WaDot built a connection. The former NP line from where the new WaDot connection starts (and ran down the hill into downtown Tacoma near Union Station) has had the rails pulled and the former ROW is pretty much getting hidden by urban 'improvements'.
My understanding is that Tacoma Rail serves the freight customers on the Prairie Line from the south end only, although I understand that BNSF handles military trains into JBLM-McChord.