is it safer to buy and download the app on the Cryptomator site (using Paddle and F-Droid) than in the Play Store? Could there be different code in the Play Store version?
AND
When I want to buy two licences, one for the Android App and one for the Desktop App to use the black theme, is it the same kind off key I’m getting or are there differences?
The Android App licence (and the iOS App licence) and the Desktop App Supporter Certificate are different things. The app licences (one for each Mobile-OS) enable you to use the apps that are provided by cryptomator. The Desktop version can be used without buying a licence. However if you want to have the darkmode theme, your support is requested by either fund the development or contribute to it e.g. by translating, implementing features, influencing or other activities. See here: Details for the Supporter Certificate.
So first I buy a licence for Android on the cryptomator site and will receive a key which I enter into the app which I will install with the APK from the cryptomator site?
Than I will buy a supporters key/licence for the windows desktop app on the cryptomator site and will receive a key to my email adress as well?
I will safe both keys for reinstall on smartphone and Desktop?
Yes that is correct.
Just for completion: If you by the app from googles playstore (or apples appstore) you will not receive a key as these licences are handled via the respective stores (as it is for any app you buy there).