Clone copies everything. It’s a mirror image basically, including hidden files which you may not see if you choose to do a drag and drop from old to new drive.
That’s my thinking
And yes that clone should still be accessible by both rekordbox and Engine prime, only difference will be the filesystem NTFS and ExFat
For example I have 5 clones of my main drive 4TB
I have 2 ExFat, 3 HFS.
At some point I even had a clone to NTFS to window proof myself incase all my MacBooks are taken aliens 
If you have the means will buy a 1tb or 2TB SSD for the ExFat job and use the mechanical HDD external for back up of the SSD.