If it's just you using the room and you don't mind, then no problem. Yes, NYC and other dense cities mean need for compromises in this type of thing.

If two (or more?) people regularly use the room and you're constantly having to push past each other through that tiny gap, then it might become irritating.

All totally a matter of personal preference. For me, I'd try to find a bed that had a smaller frame or very narrow footboard.

It's one of those "it is what it is" Either you work with what you have or get something new which will fit better and it will create more comfortable space for you.
As NYC goes, you not crazy at all, I did quiet a few jobs there and people sure know how to fit and squeeze everything in, not to mention I use to convert studio apartments by adding additional bedrooms, gym area, office, you name it, we would use pressurized temporary wall system to make 3 rooms out of one lol.... Welcome to NY!