That portion of the El was only built in the early 50's and was pushed for by Penn along with the trolley tunnel extension. The creek definitely could have been a factor though in abandoning the original portal rising from the center to one along the side, along with more empty land https://digital.library.temple.edu/digital/collection/p15037coll3/id/66093/rec/72

The point of the 2019 subway study was to avoid the CSX tracks entirely with tunnel boring. But even then they sandbagged it with extravagant stations and PIDC responded in kind by updating their master plan with 13,000 parking spaces. https://www5.septa.org/wp-content/uploads/about/2019-bsl-extension-study.pdf

Originally there wasn't going to be a 13th St station, but one John Wanamaker insisted on having a stop right outside his department store.