My brother-in-law just bought some very nice old birch flooring from Habitat, never installed. Many of the ends are a bit funky and need to be cut off. Are we better off creating a tongue-groove (he has a nice router table that should work well) or can we nail/screw down the butt ends (and cover with plugs). Not sure which is the better idea ....

Thanks!

Are the edges of the boards tongue and groove? If so, I'd tongue and groove the ends too.

Screws and plugs would hold very well and be a lot less work than milling the new T&G for each board.You may use a contrasting wood to hi-light the plug effect, or use birch so not as noticeable.
When installing flooring with plugs and screws, working for a contractor as an apprentice, we saved boxes of screws that came with the flooring for other jobs, nailing through the end of one of the boards at the butt-joint.The plugs turned out to be decoration. Nail within a couple of inches of all butt-joints and I think that would be good. .

Thank you!