I already wrote the code, added the features, everything. I could split it up into separate functions - set-waypoint-position, set-team-position, set-wing-position - but it'll just needlessly clutter up the SEXP list with extra SEXPs. I suppose I could also pop up an error message telling people to use set-ship-position instead of just doing it with set-object-position, but - why?

We've already got get-object-position SEXPs, it makes sense to have set-object-position SEXPs as well.
Except the SCP doesn't deprecate anything. We're fully backwards compatible. So removing it from the sexp list doesn't make any sense, because it will still always be supported.
But apparently it's absolutely unacceptable to have two fully supported SEXPs that can do the same thing. set-object-position does the same thing as set-ship-position and more, so it doesn't make much sense to keep set-ship-position in favor of set-object-position. I'd say just leave them both in - set-ship-position is slightly faster for setting ships and already used.