Not sure if it's already been said but I see this from an instructional standpoint. Teaching proper weighting takes a lot of time (let's forget for a moment that they should take the time to teach this) if a student is under weighted you risk two things, one them shooting to the surface halfway through the dive, and to them not being able to sink in the first place. If a student is overweight it there's a good chance we'll still be able to kick to the surface and you could always argue that they can just add more air to their BCD. Not saying that it's good practice or technique but as somebody who spends a lot of time teaching people various skills it would make teaching a lot easier.
Hopefully, with regards to PADI anyway, the revised standards and the "preference" for neutral buoyancy should push more instructors towards weighting properly instead of to do skills on the bottom (overweighting almost being a requirement for that).
As you suggest overweighting is (slightly) more preferential than underweighting in that you can increase the buoyancy underwater by use of the BCD but if you struggle to get down in the first place it is more of an issue.