Do manifest files work the same way in a Unity gradle build vs. an exported one?

Reason I ask is:

I have to manually edit the Google Play and Google Ads (Admob) manifest files to get my game to NOT crash on load. Essentially, you need to add your application ID to both manifest files now. It is added automatically to the Google Play manifest, however, it is added incorrectly <\ 123456> instead of <\123456> so it needs to be tweaked. Which is extremely not good.

Anyway, long story short, tweaking these and doing a Unity export using gradle means I can run the app OK from Android Studio. Unfortunately, running a Unity build still results in a crash, which leads me to believe the manifest merge is handled differently.

I'd upload the Android Studio version of the app but then I get a certificate error. It's like some sort of waking nightmare.