With alloy nipples, I don't round down at all, since they might break.

I usually test-fit the chosen parts (spokes and nipples) before starting, to see how easily the end of the spoke passes through the head of the nipple without the threads binding too much.
I then might drill out a millimeter or so of threads (using a drill-stop tube on the drill bit) to free up any threading that might threaten to interfere (if the spokes are perhaps chosen more than a millimeter too long).

Spokes cut on a shop machine that is well along it's service interval may tend to bind up in the nipple at full draw during the last turn of the spoke nipple. This can be frustrating and has on occasion led me to use looser-fitting alloy spoke nipples just to allow full tightening.

Some double-walled rims leave the head of the spoke nipple touching the tensed rim tape, making the spoke length more critical, in which case it seems ok to err on the short side unless using alloy nips.

Some rims are relatively intolerant of higher spoke tensions or of much in the way of pre-stressing, including Velocity Aerohead, single eyelet Module E (as well as some modern vintage-look rims). I like to check the web or check with the rim maker about what spoke tension can be used (with what spoke count) to prevent cracking (or "warp" instability) during or after building.