I would put an extra drive in each of the 7040s regardless of whether you go with the eSATA adapter cable or USB. As you said this is for a learning experience I would try the adapter, worse case scenario you are out 5 bucks and have to use USB until you get a more permanent solution.
Honestly if you want to optimize for stability and speed I would ditch the MediaSonic Box and try to move the drives into the dell servers themselves. If the MediaSonic drives are 2.5 in it looks like the 7040s have an internal bay. For the 3040s it sounds like you are only using 1 of the 2 5.25in drive bays. I would say it's better to have 4 drives hooked up via pcie then 8 via eSATA. (got the drive data via dells website, might be different)
I still use reddit for troubleshooting tech stuff and this is super helpful. That popup is so annoying, thanks.