The main purpose of clocks in guarded type theories (originating in Atkey & McBride ICFP 2013) is so that we can define coinductive constructions from guarded recursive definitions.
Semantically this coinductive construction seems most naturally modeled by the global sections modality $\square$ on the topos of trees which takes a step indexed set $(X_i)_{i < \omega}$ to the constant presheaf of "$\omega$-chains", i.e., a family of elements $x_i \in X_i$ that commutes with the restriction functions.
However I have seen very few papers on guarded recursion use this modality, instead they axiomatize a type of clocks $K$ and use the clock quantification type $\forall k. X$ for essentially the same purpose. The corresponding models are somewhat more complicated (essentially presheaves over a family of natural numbers rather than just one), and the manipulation of clocks is at least somewhat tedious, so I wonder what the advantage of multiple clocks is over using a "single-clock" model like the topos of trees and the $\square$ modality? The only paper I have seen advocate for the $\square$ modality is Gratzer, Cavallo, Kavvos, Guatto & Birkedal, TOCL 2022 but there it is just a small example.