I intentionally ride a bike that is "too big" because I need the relaxed seat tube angle. I went to a 100mm stem and it fits perfectly. It looks a little strange with such little post showing, but keep in mind this would be a normal looking setup up until the 90s. See pic.
I can only see it causing knee problems if you can't get the saddle far enough forward, but that's rarely a problem on modern bikes with their steep seat tubes. Aside from that, as long as you can stand over it without squishing the family jewels, you should be fine.