they quite literally show a popup that uncompleted quests may be broken
It is unclear which quests will be broken, or how many.
you clearly should do before continuing, like exploring the tower
How is this clear? I was assuming once I got to Moonrise it would be one long fight to Ketheric and so was trying to do everything else first, imagining it would effectively conclude the act. I had no reason to assume it would be a social zone that I needed to visit and complete quests in before doing the temple. I had no idea there would be an assault on the tower.
it’s quite clear that once you reach the gauntlet that maybe that’s a bigger thing than a simple side quest, specially when the popup shows up.
The pop-up is, but a similar popup happens when you leave Act 1, but many things remain accessible. So it is inconsistent. I think it would help to have quests show recommended levels so it is more obvious what order you're expected to do them in - you could still go out of order like you can now, but I think it would be a better experience.