No, it doesn't mean that files, etc. are inaccessible to administrators as such.
When you have booted macOS from the external drive, and haven't enrolled, you're running the default software supplied by Apple alongside your own custom modifications.
However when you're booting from the built-in drive, you're running on an enrolled installation that ...
There is a 3rd party app named Mountain which I use on my mac. It puts an icon in your menu bar and when you click on it. it will show a list of Volumes and you can mount or unmount them. The app is $6 but has a free trial period so you can test it and see if it solves your problem. See image below.
I see a drops of 17% (write) and 25% (read) when using encrypted vs non encrypted (One APFS container with APFS Volumes).
It seems that the 40% drop you experience is high in comparison, but it is hard to tell with so little data.
APFS Volume type | Write (MB/s) | Read (MB/s)
apfs | 912 | 919
apfs encrypted | 756 | 688
Using case-sensitive or not made ...