In vanilla those ships had good range and were very agile, making it hard to hit them long enough to drop their shields, and they did constant dmg to me, since they had good range and unlimited energy rockets and torpedoes.
In TC, player can get weapons with range that is greater than vanilla allowed, plus ships generally have more weapon turrets and unlimited missiles too, some with good range. So, i feel like my ships were upgraded, but those enemy ships still use vanilla weapons, actually.
Also in TC player have a lot more fighters to fight NPC fighter-shards and a lot more PD weapons, and PD is generally more efficient than vanilla, so those fighter-shards are not as dangerous as in vanilla.
In vanilla i used Radiant (and Prometheus Mk2, Dominator and several other cruisers) with plasma throwers and rapid fire lasers against those NPC ships, and they almost killed my Radiant (which is strongest ship in vanilla). In TC NPC couldn't even make a dent in my armor (which is also a lot thicker than vanilla), although i haven't used Radiant. I used Tyrant, Megalith, Odyssey, Revenant and some cruisers, because i expected a real tough fight, so i threw everything i had at them.
I`d give them at least 25% more flux capacity, to hold shields against dmg, and maybe a unique hullmods for 15-30% weapon range. This way u wouldn't have to change their weapons directly, to prevent imbalance for player, but NPC could shoot farther and be generally more dangerous. Plus its only 2 ships, so if player uses TC values for fleet size and battle points, he still have a lot more weapons in battle compared to vanilla fleet, so maybe make them 3-4 ships, or even 5?