Personally (linguistic preferences of English Language teachers aside), when someone quotes a Maharsha (or most other meforshim), I check the source to see whether I understand it the same way. I encourage you to do the same.
The reconciliation with common practice is my own; I did not see anyone address the issue. If you find someone who does, please let me know.
I do not know whether Gedolim are or were careful not to daven mandatory tefilos at mekomos hakedoshim. In case not, I would venture to say that it is no worse than any other trip. The problem, then, would exist only in case of traveling specifically for purpose of davening a mandatory tefila at that place. This is a bit contrived, I know, but at the moment I do not see another way out.