Okay. So I'm presently suffering a cluster headache so I might come off poorly so forgive anything that comes off harsh. I write this with the best intentions.
To actually get started here we go: Using different materials doesn't necessitate a change in class. There is no reason why this should be believed. If I build a car out of aluminium I have no reason to believe that it will have the same function as one of steel, or titanium. In the same way there is no reason why switching between one metal to another should alter the class. If you alter the mass and volume of the armor that is one thing, but replacing durandium, yama-dura, zesuaium, or nerimium or whatever, isn't going to change the class so long as it is just applied for the base features of the material. It's like applying an anti-beam coating like a mirror coat, or a conductive layer. It doesn't make the unit exceptionally different, just functionally so in how the material interacts.
The reason the Daisy is tougher than the Mindy is because not only is it constructed of a different material, but it is also more heavily armored. It is designed to cover more of the body, with a larger volume of material. If you melted down a Daisy and a Mindy the Daisy would have more volume. There is more to it and as such it is a tougher unit. Stood side by side made of the exact same material the Daisy and the Mindy are going to still be in different classes, in the same way that a truck and a car are the same even if they have the same materials making them up. The Daisy is bigger, tougher, and built to last compared to its dainty sister.
You reference my pointing out that taking damage to armor is varying degrees of screwed, however I specifically meant that in regard to Yamataian PAs which are pretty much glorified skin suits. This would be like comparing a sports car to a tank when stood beside a Nepleslian PA. Nep PAs are designed to have big thick plates of armor. A GM and a Player should go into the role of a Hostile or Aggressor with the full knowledge that there is a huge chunk of armor between the pilot and the core systems. This gives anyone who isn't an idiot in one of these units the capability to mitigate damage by placing the big fat plates of armored material between them and whatever wants them dead.
If a GM is treating a player or foe hosing down a Mindy, a Daisy, a Hostile, and an Aggressor with a LASR in the same way. They're honestly doing it wrong. Like... Completely missing the point of the way the units were written wrong. There is no way that one should treat the armor of the tissue paper clad Mindy the same way as the bulk and structural integrity enhanced Aggressor. The only way there could possibly be an issue with this is if you magically assume that everyone is going to be packing ordinance specifically designed to counter the Class of the foe.
Given the trend to reduce the use of weapons like the Aether Saber Rifle in combat, a crew of Yamataian PAs should be horrified at the prospect of encountering a Nepleslian PA in any environment where they can't outflank them. Even after they whittle down the Nep PA's shields the armor so long as the Nep doesn't let the Neko shoot them in the face is going to take ages longer to fell than the Neko wants. Because the armor is designed to last and take punishment. It's written into the article. It's the core of their existence.
That you're uncomfortable and think that armor is useless is honestly something I don't get. It seems obvious to me that a heavily armored Nep PA assuming it doesn't get nailed in a vulnerable place isn't going to fall easily. This is why I have repeated time and time again that this system de-emphasizes the STATS and instead makes the FLUFF the important part. We should not be judging a piece of equipment based on a hand full of numbers that we slap onto the stupid thing. Those numbers only exist to give players and GMs an idea of what sort of things they're dealing with. A guideline to stop poor players down the line from wondering, "How much exactly does this incredibly complex warhead achieve? I wanted to roleplay a Marine not a theoretical physicist!" If we expect the system to do more than tell Players what Weapon A will do roughly to Target B we're doing it wrong. Even worse we're devaluing the portion of the technology that the authors actually put effort into. THE FLUFF.
When I write articles I don't care about the DR or the Class, or the SP. I care about the flavor and feeling of the submission. I want to inspire an image of the vehicle in action. I want players to think this is cool! I want to see this in roleplay! I don't believe anyone looks at an article and is immediately impressed by the "ADR 5" notation or the "6 SP Vehicle" Honestly I would feel insulted if that was all that my work was judged by. I write articles to give an impression of a complex system the same way someone would describe a car, or a motorcycle, or a jet fighter in real life. No one is going to say, "Ah yes that F-18 is so cool because it has 13 SP" We care about the shape, how it moves, the sounds it makes in operation. Yes it is handy to know that the missile payload can leave a tank as a flaming husk, but the how of that is much more interesting than the statistical aspect.
TL;DR - The Damage Rating System is a guideline to help GMs and Players get a general idea of what will be effective against what. If someone ignores the huge body of text that describes how something is built and functions, and instead focuses on the little numbers and decides that a Mindy and an Aggressor are able to take the similar amounts of punishment and suffer similar effects I honestly don't know how to help them apart from pointing them back to the article and demanding they re-read the fluff and question how the hell they thought such a light unit could possibly reflect the performance of something over four times its volume.