It's an element or compound that hasn't been discovered or invented yet. In my thinking, those are both natural substances - we have elements and compounds in real life - and haven't discovered them all yet. Magic entails the supernatural; things that do not exist in nature, and never can. So even if dilithium is non-existent, it can be still be intended as a fictional natural phenomena, just as Sherlock Holmes is a fictional natural character.
To put it another way: If something was magic, simply because it was made up, any device that does not exist in fiction, including genres like the detective novel, or spy novel, would be magic.
I think you're realllllllyyyy stretching there...
