Considering shows with lesser budgets manage to fake their logo on buildings, it doesn’t seem like money would be an issue in making it happen, so Loeb’s reasoning may be legit.
Whether or not fans believe Jeph Loeb’s response that the shows intentionally left the tower out of shots to help “show this could be on any street corner,” is another issue.
It could also be that someone just never thought to include it, and Marvel saw fan complaints and have had guys like Loeb trained with this response should it come up in an interview.