RDM950 The F-Droid variant likely has less potential for trackers. I've used both and without actually looking at the source code, I've never been able to distinguish the difference in functionality. I usually opt for the F-Droid/FOSS variant of things when available with some exceptions. If you notice any issues, perhaps like missing notifications (unlikely), then try the Play Store version instead. Again, just import/export the OPML to switch back and forth.
Some apps like Maps/Navigation apps, like Organic Maps, usually can't work with Android Auto unless you install them from the Play Store.
Some apps remove features on the F-Droid variant due to containing proprietary components, which you may or may not need, so it is best to look into differences in apps before each initial install. If you're installing apps from F-Droid directly, some apps aren't official apps, but community variants. For example, Joplin's F-Droid app is not official and often delayed, which could cause issues when trying to sync its content with an official Joplin client.