That's actually how it works in the
real upcoming rewrite. You bring the Omnifactory ships, it starts analyzing them (this takes much,
much longer than in the current version, but every additional ship of that type you sacrifice halves the remaining analysis time), once analysis is complete you have to queue construction manually (requiring supplies plus metal/rare metal/heavy machinery depending on the blueprint). There's an upgrade that allows remote communication with the Omnifactory, so it's not as annoying as it sounds (did I mention the rewrite has an upgrade tree?). Weapons/fighter wings are still auto-produced the same way the current Omnifactory does them because nobody wants to micromanage to that level.