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Unix Pageant has a variety of different options to control the
lifetime of the Pageant process. One of them is -X, aka
LIFE_X11 in the source code, which causes Pageant to
connect to your X server as a client, so that when you log out of your
GUI session and the X server terminates all the client connections,
Pageant will take that as the signal to shut down.
If your GUI session is not based on X11, this can't work, of course. In particular, we have no analogous mechanism for detecting the end of a GUI login session hosted on pure Wayland.
I don't know enough about Wayland to know the best way to fix that. Pageant's X11 lifetime support works by using the from-scratch X authorisation and setup code that PuTTY uses for X forwarding; for Wayland, we'd either have to write some fresh code to speak the Wayland protocol, or else link against at least the lowest-level Wayland client library available.
For extra credit, it would be even better to autodetect which GUI technology was available, so that users didn't have to guess the right one in their startup scripts. I don't know how to do that either.