Honestly, armor means that mk1 fighters do nearly nothing to any starship, while mk3s are actually extremely powerful.
Consider a ship that does 600/1200/1800 damage vs armor 1000 (generally the lowest found on any guardian ship) with no ship-type-bonuses
This means mk1s do 30 per shot, mk2s do 200 per shot, mk3s do 800 per shot.
This means one mk2 is worth 6.66 mark 1s, and one mk3 is worth 26.666 mk1s
Now lets look at it with a 4x bonus vs that ship type
damage becomes
1400/3800/6200
Thus a mk2 is worth only 2.7 mark 1s, and a mk3 is worth 4.4 mark 1s. The huge spread disappears into smoke and the balance comes back into it.
So, really, what I'm saying is that with the current implementation of armor, higher marks are always ->vastly<- more beneficial, to the exclusion of the lower marks even being worth building. To the point where once you get mark3s, ignore building mk1s and 2s, they're simply a waste.