Epoxy suitable for wetting out composite material is not brittle. A carbon bike is technically a continuous Epoxy coating.
There would be no reason for it to crack or flake unless you actually break the frame. A thin layer of Epoxy does not weigh a lot. It's just easier to coat the sanded lugs and continue with the coating onto the rest of the frame.
I don't use WEST but the unsuitable for clear coating remark has to do more with the clarity of the finish. That's for when you build a wooden boat and want it to look like it's just wood.
When you're wrapping carbon lugs you want the slowest hardener you can get to allow more working time anyway.