Signal is not distributed outside Play store and signal own website. If you downloaded from F-droid, its probably from Guardian repo.
If you download it from play store, signal will update through play store. If you download it from signal, it will update through itself. If you download it Guardian repo, it's basically the same downloading from signal website, it will update it self.
The thing you can do is just basically turn off the update notification and just update it from guardian repo. Or just disable the guardian repo and let the signal update itself.