I don't know shit about plural systems and have no idea about PluralKit but I can already forsee two issues that regular user accounts would have:

• There may be systems who switch operators frequently; having to switch between multiple accounts could be a major hurdle for fluent conversation
• Some systems may have too many operators to reasonably manage accounts for

As far as I understand it, PluralKit is more of a hack for acting as multiple pseudo-accounts with the convenience of a single (platform-) account. Given that Matrix, Element and the like are FOSS, it ought to be possible to build such a convenient single-"user" multi-account mechanisms into the clients or even protocol themselves rather than relying on hacky 3rd party add-ons.
Especially given that the user base of Matrix is far more likely to come into contact with plural systems than the general population is. (In the communities I frequent, I know of at least one and would not be surprised if there were quite a few more.)