Ah, oops, I assumed the boost was cumulative 
Still, does that look like a reasonable number of flagships?
If they properly sacrificed the opportunity to get additional starships or guardians or fleetships or a golem, then yes, that seems reasonable. (What difficulty are you playing again? And what scaling of the exos?). However, knowing whether it payed for it properly or not is hard to tell without logs.
Now, it could be argued spending most of its points into 59 Mk. I flagships was a rather dumb choice for a unit composition by the AI. Maybe that could be addressed.
Or it could be argued that the exo-cost of the Mk. I flagship is too low for how much it brings. Well, it wouldn't be the only one. Exo-costs are really in a strange place right now TBH.