It was an improvisation, the Condor wasn't a bomber as we know, it was a "very long range" prewar airliner, built to break records but not to take gunfire or combat stresses.
It wasn't about a strategic air force, it was about a maritime one as again we know. Germany had neither a strategic air force nor a maritime one, shocking oversights but reasonable in the industrial environment. The Kriegsmarine had no dedicated air force, the Luftwaffe had to compensate and you have the issue with interservice rivalry for industrial resources in Germany. The Luftwaffe did not want to be subordinated to the Kriegsmarine, the system only worked well in limited engagements involving specialised, small unit formations like Fliegerkorps X. They were given unusual latitude for this role.
The Fw-200 combat modification then was a matter of utilitarian use of a surplus aircraft type valuable enough to a Navy to provide a strategic asset. It wasn't designed for it neither was it very good at it, but it was available and could do it. In a time where the Baltimore was a major British maritime bomber, the Condor seems amazing, but it is not a B-24. To the rest of the Luftwaffe the Condor, in the miniscule numbers it was represented little more than an addition to the transport fleet. So maritime bomber it was. Suits it, they don't normally fly over FlaK, and would never stand up to even a near miss if they did.
Biggest drawback was being a civilian design without being propaganda, really it was just an airliner, all the fuel lines were on the underside of the airframe as opposed to military aircraft which would protect them from groundfire. Rifle calibres with heat-tracers could bring one down if you hit it right. But ships/boats aren't exactly stable AAA platforms.