My take:
Augmentations are cyberware, bioware, drugs, sustained spells, and adept powers. The general rule of thumb: if it counts against the augmented bonus limit, it's an augmentation. Of course, that rule of thumb begins to get VERY complicated when it comes to skills, at least in 6e. But, attribute-wise, at least there it's still fairly cut and dried

Either way, dermal deposits is (imo) not an augmentation, for whatever that matters.
Also:
Xenon is absolutely correct in that 6e cut so many corners in slimming down, sometimes you just have to look at 5e to figure out what they mean in certain contexts. But, on the other hand, sometimes an omission is deliberate. It can be challenging to tell when an omission is an oversight or a deliberate change. Dermal plating and orthoskin no longer saying they are incompatible with Dermal deposits could seriously be either.
My opinion:
Just let them stack. Dermal deposits is giving you all of +1DR higher than you would normally get on top of your augmentation, that's not breaking game balance. The other benefit to Dermal Deposits, turning unarmed damage from S to P, is likely already made moot elsewhere by some other augmentation anyway if you're building a combat type. While it makes a degree of sense to say you have to lose the natural body part (like, as Xenon points out, if you have the Low Light quality you should lose it when you get cybereyes) it doesn't seem like it's worth the bother to say you lose Dermal Deposits if you implant Plating or Orthoskin. Of course, there's nothing wrong with saying you DO... I mean, if you get 2 cyberarms, 2 cyberlegs, cybertorso, and a cyberskull, what's left to still have Dermal Deposits? The concept of losing the quality due to an augmentation replacing them IS sound... as I said it just doesn't seem there's (much) of a game balance point in saying so in this case. YMMV.