Do you paint your engines fully assembled?
A lot more masking if you want to paint major assemblies separately. But there are some brackets, bolts, etc. that may want to be a different color, or that get in the way of a good spray, that you can easily do separately. IME if you don't paint the bolts they just get rusty, unless you are talking about environmentally-controlled storage, which I don't have.
I admit my last motor was rather quick & dirty...