Apps installed from the developer's website or Github repo or similar can have the same signatures as the Play Store version. (F-Droid versions always have different signatures because they are built by F-Droid from sources, not by the developer.)
In Google Play Store there's an option to allow Play Protect to detect all apps on the phone, not only the ones installed through play store. AFAIK that option is enabled by default. If that's allowed Play Store offers updates for these detected apps if available (and they have the same signatures as written before).
Maybe you could prevent updating these apps by just disabling the option afterwards.
To prevent app detection through Play Store from the beginning, you should disable this option immediately after logging in into your Google account on the phone. And best way would be not to have installed any other apps from other sources before disabling that option.