No. /e/OS developer do not alter the apps that come through the App Store. You can check this using a PGP signature check, or a checksum.
We also do not share any inputs with google regarding this. The point to be noted is if a user is installing an app like WhatsApp or Facebook on top of /e/OS then their information is for sure going to pass on to Google through these particular apps. Also not all apps that can be installed on /e/OS will work as some have a clear dependency on Google code. You can find a list here.
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