Android apps are becoming more and more dependent on the closed source blobs that Google ships with Android devices, so some apps might not work without them. Although microG exists, it isn't perfect and some apps still won't run with it.

A Linux phone can forgo Google's userspace libraries for Android, and if they're really needed, Android can just run in a container like with Anbox. Instead, it can ship with the typical GNU, busybox or ulibc userland that most Linux users are familiar with.

Also, you can use pretty much any language or runtime to write apps for Linux, while you're stuck with the Android Runtime, Android NDK and Java compatible languages and runtimes on Android.