In my opinion, an atheist can, but probably wouldn't accept Plantinga's account of warrant. To clarify what is being discussed, here's a formulation of Plantinga's warrant taken from a summary of his second book:
Cognition must be functioning properly (and functioning for the cognitive environment for which it was designed), the original plan of design must a good one, its relevant modules aimed at truth, and the objective probability of a belief being true (depending on all these underlying factors) must be high.
Although the word "design" is used a number of times, that does not in itself infer God or an intelligent designer. Design can come from undirected processes, which is the contention of Darwinian evolution. Another example of an undirected process that produces a functional design would be a river bed. Nobody tells the river where to flow, but the process of flowing haphazardly produces a path that efficiently moves water from high to low ground. It is a design in a sense, but there is no intelligent designer.
The difficultly Plantinga addresses, however, is how one would produce a design for a truth-determining mechanism such as a mind. It would seem that if the second and third criteria (a good original plan and modules aimed at truth) were denied, the final criterion (high likelihood of producing truth) would be denied as well. And it seems unlikely that any unguided process would be a good plan for producing a functional mind or that modules would be directed at truth rather than, say, fitness in the evolutionary sense.
But an atheist could suggest following Plato that Mind exists as an abstract and that our minds imitate or mimic the form of Mind. To put it in the terms above, the form of Mind is the original plan (and it is a good one) and the modules of minds aim at true because they mimic the modules of the form of Mind. I see that type of thought in the works of Douglas Hofstadter, for instance.
I'm not aware of any atheist thinker who does accept Plantinga's account of warrant, however. It seems to have been designed to counter the idea that since we have the mechanism of evolution, we no longer need a theory of epistemology besides the assertion that evolutionary processes must result in better and better minds.