GPlay version is also ~40MB. There’s no difference between them, except that Gplay and Github version are built by the developer.
Use F-Droid version, of course
I think what you mean is that the versions are different. The one on Github is the most updated as the developer built it themselves and uploaded instantly, while for F-Droid, it has to be built by the F-Droid server and takes time and I don’t know much about the Play Store. As @Morgoth said, the F-Dorid version isn’t built by the developer, the signing keys are different and cannot be interchanged, means you cannot update on top of another version without the same source (Github and Play Store the same).
Nevertheless, I do recommend using the F-Droid version as it is signed and checked so that it is built from source despite the fact that it’s slower.