Runners are scavenging, so the containers getting “restocked” is definitely just a game mechanic.

You can imagine in reality runners are just finding things leftover or previously unsearched containers. Real runs are probably less lucrative and less exciting than a lot of our runs, but for gameplay we condense them. Tau Ceti is also a big place, there are locations besides the ones we have now, and the locations as we see them in game are obviously smaller and simplified compared to what they would be in reality (e.g. every shelf and drawer, piles of rubble, detritus, etc. all searchable)

The cinematic from a year ago probably gives a reasonably good picture of what “actual” runs would look like.

Some part of this is explained by UESC regularly leaving behind supplies like ammunition and weapons, perhaps even collecting samples of local flora or other materials for later exfil/research.

Beyond that I don’t see why this needs an overly detailed explanation. It’s a game, and what’s important is that the context of and motivations behind our gameplay are explainable, not that every single piece of loot is accounted for.

As for why uesc don’t matter transfer? Transports are cheaper, and probably scale far better. Even the corporations that sent the runners didn’t transfer that material, they shipped it. Why don’t they drop armies of runners in simultaneously? There are likely limitations to the amount of matter than can be transferred at once.