What value do timegates add to video games?

Well, if taming dinos in ARK was instantaneous, it would massively change the game, and turn it into nothing but a constant stream of t-rex (or other large predator monster) battles. Those 1-hour countdowns are a time-gate for balance.

If reloading in CS:GO was instantaneous, there would be no tactical decision around when you do it, or danger presented by it happening at an inopportune time. Those 3-second reloads are a time-gate for balance.

There are tons of time-gated mechanics across all sorts of games. You just don't like this one.

How does the user experience improve or degrade if the wait is [less]?

Well, it means that other players may have to contend with them too-quickly returning to a fight as though nothing happened, which would be pretty crappy if you just got finished killing them. It would mean that if you fly across the solar system in a ship with a very fast Quantum Drive, you could potentially just summon your large, slow ship at your destination, effectively obviating the difference in travel time.

What’s the difference between acceleration humans can’t survive and wait times? What’s the line we can’t cross to suspend disbelief?

It's not about realism, it's about game balance. Your ships are something you need to take care of. Dying is and will have major consequences (loss of items, for instance). Do you think that Eve's manufacturing timers are about realism, or that they are disrespectful to the players? Should a tiny shuttle take the same amount of time to build as a Titan (the largest ship class in the game)?

It's game balance.