Usually built in standoffs are placed in standardized positions and are/should be used. I have yet to come across a tray that had a built-in standoff in a "wrong" area. If your concern is the width of the built-in standoff, again it will be within specifications as to not cause a short - I have seen them 1/2" and no issues. Note also that your standoffs are grounding points for the motherboard so, if you are concerned and do feel the need to put electrical tape over the standoff, make sure there is some metal continuity though the screw at least.
If I misunderstood, please clarify.