The AOSP keyboard was available on f-droid when I installed f-droid, and the f-droid app kept nagging me to replace the keyboard app on my phone with the debloated AOSP version from f-droid. Debloated, in this case, meaning without support for minority languages such as mine.
There's nothing intentional there. If the keyboard you had installed was also distributed via F-Droid using the same APK identifier, then F-Droid just detects an update since it's the same app.
To prevent this (it can happen with most apps distributed both on the play store and F-Droid) you can tell F-Droid to ignore updates for a specific app.