Infinitesimal analysis (by which I mean that originating from topos theory---not the nonstandard analysis of Robinson) seeks to recover the pre-limit notions of calculus (which are sufficiently useful to persist in applications and intuition) in a formal way by throwing out the law of the excluded middle, which led to the paradoxes remedied in the 19th century.
My question relates not to the theory, which is certainly able to be constructed from scratch, and, rather, with how the models by which we're assured of the theory's consistency are founded.
As I understand it, from what little I've read of John Bell's 2008 monograph par excellence, these models are toposes into which it's possible to embed $\mathbf{Man}$ without introducing nonsmooth entities. However, if our goal is to completely supplant limit analysis (for, say, pedagogical or constructivist reasons; it's a noble crusade either way), it seems like this is a dependency loop: we need machinery to define $\mathbf{Man}$ as "the category of smooth manifolds and maps," but the entire utility of atlases is their reduction of computation on manifolds to flat analysis---which is what we're trying to replace.
Is this actually a problem? Is it known? Tractable?