Yeah those are very fair counter arguments and i agree with them. With my lack of modding experience i can't offer any solutions or suggestions on the modding side and it's quite commendable that you're thinking about the end user. Even still i think it's worth talking about just in case something comes of it.
I've played around on my end and had a few ideas pop up. Quite a few of the ships in the HM games have weapons at the top and bottom of the ships such as the Flak and Assault Frigates, both Vaygr and Hiigaran destroyers, Hiigaran Battlecruiser, etc. What you could do is give them the weapons mounted on the bottom of the ships as invisible mounts, give them a few small mounts for PD that are similarly invisible as well. Or perhaps none at all.
These few extra mounts could make them good enough for their new class and create a new "Dynamic" for the mod. With weak/non-existent PD you could make it so the ships from your mod rely heavily on escorts. Although it might be very difficult to make the AI cooperate.
Let's use the Vaygr Destroyer as an example since we were talking about it. Giving it another large slot makes it similar to the Dominator in vanilla with 2 Large ballistics and 2 mediums plus it's integrated missile launcher. However, it's worse PD and weaker armor would make it vulnerable despite it's better speed and maneuverability, especially against carriers.
However, let's say our Flak Frigate or the Hinsra has another medium mount, invisible as it's beneath the ship Lore-wise. It could mount two Flak Cannons or Dual-Flak Cannons, or whatever else that fits and act as an escort.
On paper these two could work perfectly in conjunction but i doubt it would work perfectly due to the AI and it might lead to the ships being overly specialized. Plus fitting in extra invisible mounts might be an absolute pain.
Basically, adding a few extra "Invisible" mounts might make up-tiering them easier, the lack of PD slots might allow the smaller Frigate and Destroyer class ships to act as escorts. However, everything you said is still very valid and the whole up tiering idea might not be possible, just throwing ideas out there.