Here's one way you can modify the damage between races, physically (and even magically) without ever needing an (obvious) attribute! A slight racial coefficient in the damage calculation. Just enough to vary it up or down a bit, make a given race a bit more optimized for a given skillset and method but not so much that it renders your character ineffective if you choose to follow a path they're not directly suited for. In fact, I might suggest ONLY bonuses, rather than penalties. Voila, racial differences in ability without the need for an attribute system, and also that won't be superceded by just focusing more on the attributes you lack. I mean, at the absolute peak of physical capability, I'd still expect an orc to outmuscle a bosmer, or a spindly altmer.
As for perks and attributes, no, perks don't make attributes redundant. However, their implementation in Skyrim means they can possibly do the job of attributes better than attributes themselves, simply because they can affect things in non-static ways. An attribute never changes and doesn't make any significant changes to your gameplay beyond increasing any value it's connected to. So while perks don't make attributes redundant, they have another quality that allows them to be an effective replacement (and I'll remind you that increasing attributes was also a reward for increasing your skills, not just something unrelated that happened when you levelled up) - they're more versatile. They can do, quite simply, more than a flat attribute system ever will be able to.