Hate to break it to some people, but it is not at all unrealistic or immersion-breaking to have an EMPTY tag on containers, at least most of them. In fact, just the opposite - it makes far more sense from a realism standpoint. This is because it is far more likely that you would see that a container has already been looted/emptied just by glancing at it than needing to bother to actually open it yourself and check closely.
The one thing that could be argued is that alternate visuals would be nice, but that's a matter of reducing assets. It's the same as Oblivion not having separate visuals for harvested flora but modders adding it (and then BGS including it in Skyrim because it was popular and they managed to fit it in while cutting other stuff). For containers, modders have also done things like animating opening containers or adding visuals of open containers. However, we do not yet know if BGS has added such visuals to FO4; they may have, after all. It would also be nice to have relatively untouched containers plus containers that have obviously been hacked open or whatever. However, this is an RPG. Players are supposed to use their imaginations. Therefore, having everything explicitly shown is certainly not necessary. That is why it is false to claim that having an EMPTY tag in any way undermines immersion or realism when in fact the opposite is the case... IF players use their imaginations, of course.
Frankly, the "looting on the fly in real-time" doesn't matter that much unless you have a very high encumbrance, and I seriously doubt that that will be the case as BGS has never had high encumbrance. Loot a couple of things and suddenly you're a sitting duck, so I don't think many players will be able to exploit the mechanic very much. Instead, it's far more likely that they'll need to clear an entire area of hostiles and then loot. At that time, looting on the fly in real-time simply expedites a process that quickly becomes tedious.
Ultimately, we'll have to actually play the game, but I doubt it will change much.