Anyhow, I am currently on my second game, the first game with all expansions turned on. Is it normal or okay to want to do all of one's fleetship manufacturing from Enclave Starships?
Anything's okay so long as it works for you. I've personally never heard of someone doing that since factories are free when it comes to knowledge (10k to unlock up to mk3 enclave, 20k for mk4 enclave), allow rally points, are cheaper to build, and can have more built. They certainly have their uses on occasion. Do you use enclaves to reinforce your units in the field?
Also, merc ships are just way too expensive for the early game - as others have said, I rarely have the kind of resource flows where I can throw away 480 metal/crystal per second, but that's probably more because I'm constantly having to rebuild my normal fleet early game, and later game I'm trying to maintain a couple golems, a spirecraft fleet, and my defense infrastructure.