Paragons are supposed to be the epitome of domain design.
And the templar faction is meant to be far superior to anything the domain of man ever even dreamed of.
Like I said originally though, the problem is indeed with the balancing of how certain vanilla ships such as the paragon synergize with high character level benefits all stacking together.
I'd certainly like for the most optimally fitted paragon to still not be capable of taking on 3 optimally outfitted templar paladins (and any nearby jesuits+bulwarks) simultaneously without breaking a sweat, but it's the mod maker's prerogative if he wants to bother trying to balance his mod against vanilla content that is clearly not yet balanced, itself.
I don't think it would take much more than something like allowing templars the ability to deal some percentage based flux damage, and maybe some additional speed/maneuverability (high level character skills allow for enormous boosts in speed and maneuverability to even hulks like the paragon and onslaught, already, allowing even them to kite enemies to a degree), but I definitely wouldn't blame dark.revenant if he just chalked those factors up as unbalanced outliers that should be ignored until starsector devs officially address them.