I think you are correct about no real legal reason not to possess most of those LE only marked boxes. To the best of my knowledge, which is just that ( I certainly could be wrong) most LE only markings are much more of a company policy, than a real restriction. I am not aware of any law that would make it illegal for a non-LEO to possess them, unless it was perhaps some local type of restriction.
Usually the rounds with that marking on the box are still offered in quantities of 50 instead of the much more common 20 or 25 round packages. So that may actually be a simple designation some manufacturers use as well. But even when using the ammo contract, some of our handgun ammo boxes were still 25 rounds, depending on manufacturer and caliber.
The only round I am aware of from personal knowledge that was ever intended to be restricted from commerical use was the old Treasury +P+ loading, back in the days before +P+ loading were commerically available. From memory that was at least 15 or 20 years ago, and probably even longer. That may be the only "restrictively marked box" I have never seen on a dealer's shelf.
That one came in a 50 round box, mostly white, with large lettering stating it was only for law enforcement use. Those markings were actually more prominant if my memory is correct, than the actual caliber designation was on the box. The only way to obtain it initally was for federal agencies to order it with government funds off the Treasury Ammo Contract that Secret Service negotiated with all manufacturers for a 5 year period. So if it started showing up on gun store shelves, someone could very well have a problem shortly thereafter.
Just thought I would offer what I could on this subject.