I don’t think it’s needed. As you say, if it was present it would contradict the statement that the PEP doesn’t say how package managers should handle TUF.
On the other hand, it says so little (basically little more than “if you support TUF it should be on by default”) that I can’t really get excited either way
More broadly, I don’t think that “transitioning users” should be a concern for the PEP. For all practical purposes, whether TUF is in use is intended to be transparent to end users (if the package manager they use supports it, things are safer with no visible impact - much like https vs http). So what’s to transition?