macOS not allowing me to restore media files from one external drive to another
This seems to be a bug with macOS Mojave. Even I tried to do the same. I came across the same errors you are facing. Luckily, I was able to clone the disks  which is same as restoring. 

There are several ways to clone a disk. You can use some utility tools available on and off the macOS App Store.

I tried this https://www.shirt-pocket.com/SuperDuper/SuperDuperDescription.html cloning utility to clone my main drive to an external SSD both having the same partition map - APFS. This should solve the problem.