Eh, we were asked to make a bio-survey ship. Starfleet has all the information we do and they haven't told us to abort. I'd imagine they'll be pleased our ship has greater firepower, as it can stake a claim and defend it, but San Francisco will be making an alternate design, perhaps a warp 8 patrol destroyer or combat ship to do the things our design won't.
Ultimately if our design isn't ideal, Starfleet won't make many and will make another design instead. It's not like they're stuck making 3 tranches of Project Darwin to the exclusion of all else.
Besides, we don't know for certain what state Starfleet and the Federation will be in post-war, we can design our next ship in direct response to that. We'll also hopefully have better weapons and shields, so any design we make will be fundamentally stronger than our current ones anyway.
Ultimately if our design isn't ideal, Starfleet won't make many and will make another design instead. It's not like they're stuck making 3 tranches of Project Darwin to the exclusion of all else.
Besides, we don't know for certain what state Starfleet and the Federation will be in post-war, we can design our next ship in direct response to that. We'll also hopefully have better weapons and shields, so any design we make will be fundamentally stronger than our current ones anyway.