You want to compare optimally built ships because that's what you will be putting in your fleet. If you have the option of putting a medusa or hammerhead in your fleet, you will be outfitting them both as best you can, so you should compare their best versions. As to whether a 1v1 is a good comparison in the first place, that's much less clear.
I think the hardest part about OP balance is that sometimes ships feel like they don't have enough OP to fit stuff but are still really strong (astral) because they have stats/systems that are really strong and on the other hand I would say the wolf has a reasonable amount of OP but it's stats are just too weak. So ship balance and OP are not really directly correlated, but it still feels bad to not have enough OP, even if the ship is strong.