Can a long stem be used safely with a short head tube? I picked up a 91 Rb-1 50cm down tube and 53cm top tube but the reach is a little short. A new stem was my best option so I picked one up. the height of the stem seems too long visually for the head tube but feels better. I understand the handling may be a bit different but would like to know if its safe?
If the quill stem is in the steerer tube at or past the minimum insertion length then mechanically this should be safe regardless of the height above head tube. This is assuming that the bike is still running a threaded headset and quill stem and the headset was correctly fitted with the fork.

I can't comment on the effect on handling and how safe the bike is to ride now.

Great bike by the way.