Most editors tolerate the type of word repetition you described in grids mainly because multiword expressions are preferred to single word entries ... and most of the former happen to involve short words like up, the, and, on, to, etc. I like to think that any word that wouldn't be capitalized in a book title is fair game for repetition in a grid. (But, one would not want to have a stand-alone entry like OVER in the same grid as HAND OVER). Applying the above guidelines, one is probably OK with TURN IT UP in the same grid as BUTTER UP, but one wouldn't want to have a grid which contains both PAPER OVER and WAX PAPER. I hope these examples help.
Keep in mind that most of the "rules" of crosswords are designed to provide a certain aesthetic ... or to weed out blatant sloppiness from constructors. Since lively themes and lively fill are eminently important, the remaining guidelines are there to provide depth. Sometimes guidelines are going to be violated while constructing, but if you violate too many of them their cumulative effect detracts from the overall aesthetic... and that's when you run into trouble.