As to Partition E, I believe I should, for the purpose of defrag'ing with MyDefrag, consider it as a "system disk" even though I don't boot from drive E. Am I right?
Yes, in your case your E disk should be treated as a system disk. Please note that the automatic MyDefrag scripts (used by the scheduled tasks) do not use the choices that you make in the MyDefrag script chooser window. You will have to edit those scripts by hand to have the E disk processed as a system disk.