There's much to be said for stuff happening over time and timelines of events unfolding. The problem is when you start to replace time tracking with other causal mechanics. A problem that happens in 3 days is very different from a problem that happens in 3 checks.
Sure. But sometimes that’s exactly what you need. This pillar is crumbling and it will collapse if hit three times, otherwise it will collapse in 300 years. The negotiations are a success or failure after three checks, or the other party loses patience and leaves after three hours.
That, and a generic system will produce different results than as bespoke subsystem.
Sure. But there are three important questions behind that: 1) are the results different enough to really matter, and; 2) what is gained or lost using a generic system vs bespoke subsystems, and; 3) how much word/page count and brain space are you willing to sacrifice for those bespoke subsystems.
To me, the difference almost never actually matters. For example, towards the end of my time running 5E I stopped using hit points for monsters and used hits. A simple clock mechanic that took a paragraph to detail, but replaced dozens of pages of bespoke rules. For a time I tracked HP also, to see how close my clock system was to the official rules. About 80% of the time my clock system was spot on. Though, on a few occasions there was variance in both directions, about +/-20%, well within the range of rolled HP. So, while clocks did not exactly reproduce the bespoke subsystem, they did replicate it well enough. And it was dramatically easier to use and keep tract of.
This also had the benefit of giving me a system for knowing how difficult the monster would be as a non-combat challenge. It told me how many checks the PCs would need to overcome the monster. I gave the players a peak behind the curtain and they immediately started trying other things than just attacking. Want to bribe the monster to leave, that many checks or the equivalent. Want to persuade the monster to fight beside you, that many checks or the equivalent. Switching to clocks improved my game and opened up all kinds of non-combat possibilities.
I’m a fan of lighter systems and frameworks. So I prefer saving dozens or hundreds of pages on bespoke subsystems when a single generic one will do just as well.
Using clocks, I replaced the damage subsystem, the social subsystem, and added in negotiations, bribes, and anything else that could be covered by clocks. And all in a paragraph or so. I’d say that’s a huge win for clocks.