Interesting! Let me address some points! Maybe add some of your points to the OP! Including removing the DT portion of Pet food. I think giving our Buffalo 10% PDT under 50% isn't that broken however, So i think it'll remain.
Firstly, I went ahead and edited a few things in the OP For you. You make reasonable arguments even though it sounds like passive-aggressive Sarcasm at some points... But i can let that go cause its probably not on purpose...
Anyway, Addressing the Roc Issue. There is an Evasion Cap, for Enemies and Players. And On a lot of Mobs, Dipper Yuly can reach that with Atmas. Without Atmas, Side-By-Side, Dipper Yuly and the Roc pet would have the exact same EVA Before training. Through Training you can raise your Rocs EVA 15%, thats if you feed it the same Pet food Every day, its not absolute. Some would maybe give him Attack pet food. So he'd possess the same EVA as yuly, but stronger hits. 15% Attack won't take him from hitting ~150 to 300, So its not going to be That overpowered. Perhaps the Roc could simply maintain a Triple Attack as a Bonus-trait, and just be a WAR/WAR, letting Dipper Remain King of EVA Tanking?
On the point of TP moves, As a BST you should already know well that just because the mobs very of the TP move is powerful, that the BST pet version isn't always going to be as broken. Buffalos TP moves are actually quite weak, the only problem with some of them is that they have Added Effects. Snort ignores shadows, the Stomp-move Paralyzed. These could easily only do the same damage as Foot Kick, or Lamb Chop. Triple Attack can do crappy damage as well. Just because it seems nice on paper does not mean it needs to be overpowered. Triple Attack could easily land in the same general damage fields as Foot Kick, etc.
Also, as for the Plague move, It could easily be resisted by HNMs as some of our TP moves do, but also have lesser impact. Wild Carrot can heal some Rabbits for 2k~+, While our pets doesn't. in the same light, Plague could only inflict ~3tp/3mp/tic instead of what it is from the Enemy! Just because it might seem OP'd, Doesn't mean it wouldn't be a good addition. It can be resisted as well. Pets need their uniqueness. Plague from Buffalo is that as well.
the Immunity in Abyssea with only 1 atma brings a solid Point, and as i said above, I have adjusted the Training because of that. You made a good point there, it was something i overlooked. But there is a silver linning. If they were to chose that Buffalo because of the Above, It would keep other DD jugs useful, as they would be silly to use the Buffalo, a Low-Dmg out-put PLD, as a DD pet in say, Exp parties. Since the Buffalo pet I would imagine doing less damage over all than other DD pets, Simply more defensive.
I don't think i can address ALL your points in the OP to clarify, So i hope people will read this as i type it here.
For all intents and purposes, Think of the Special pets DoT/DPS like this. For comparison, Lets assume that NuseryNazuna hits the mob for 150. so as a comparison heres what, before training, the other pets would do.
So as Reference:
Nazuna - 150
Roc - 125
Buffalo - 100
Malboro - 175
Wamoura - 125
Peiste - 130
Orobon - 110
So Before Training, They would average @ or Around the normal pets. But each one would have its own unique aspect as to why you would use it. Also to keep it from completely obsoleting other jugs. It could have a 1 hour Timer, and Be linked to our 2 hour, So we could only maintain this Pet for half the time, Realistically. (in Abyssea with 2hour resets though, Another story). But the mobs are to the point, They would not be So powerful other jugs are obsolete. (for instance, if you built a DEF Buffalo as listed in your example, You wouldn't use it for Exp/DD purposes. it would be silly, hes got less-damage-hits).
I hope i explained that well, I probably missed a few points. I'll look forward to your response.
Edit: And one needs to remember, Inside Abyssea you can abuse a lot on BST, including the Full 100%PDT. But what Cant be abused in abyssea? We also need to think of these pets in term of Post-Abyssea. We don't want our pets to be so weak inside Abyssea as to prevent abusing Atma system, that when we step back into the real world they are too weak as well because they would have to be Nerf in order to not Abuse the already very abuseable Atma System.. Achieving a Balance of Usefulness without Overpowering is Very difficult. But with a lot of Tweaks i think it can work.
Now do i expect to get any Attention to this Idea >.>? Probably not...