When Kant talked about apriority in the realm of physics, he was talking about background principles being a priori. Science as a whole is like an experiment about the relationship between mathematics and nature, an experiment to test this relationship. (So far, the experiment is going really well!) Experimenters might or might not make or recognize the non-experimental components of their programs---beliefs about inference structures, modality, intuition, etc.---so they may have an appearance of doing science without any question of epistemic apriority. But Kant thought reality as we know it was too orderly for that: there are arguments to be made and decided about some of the background questions, and these can then go on to color the conclusions of our specific arguments about physics.
The notorious case is his doctrine of space and time. His objection, if he would have one, to some of the ways the issue is nowadays framed, would be not so much that we couldn't discursively represent various systems of geometry, applied to spacetime. Remember, this is a man who suggested that time itself being one-dimensional is contingent in an abstract sense. Time as we know it flows along a one-dimensional line (or so it seems), and is subject to the mathematics of a one-dimensional line as such. But we can at least imagine in logical space (but perhaps not in concrete imagination, mind you) a form of time with the mathematics of a two-dimensional structure, or in three dimensions, or whatever.
The next question is whether the above quasi-objection tells against the modern rejection of Euclidean limits on geometry as applied to physics. I don't know that our intuition of space is actually limited in a Euclidean way. I would say that Kant was wrong, not about whether an intuitive spacetime is a fundamental background, here, but about the particulars of that intuition. If physics needs a non-Euclidean geometry because there are some physical experiences of non-Euclidean structures, that seems to me to indicate rather that we do have an intuition of space as such: not as if as humans recently evolved to gain the ability to perceive and visualize non-Euclidean geometry, then!
More broadly, we do have plenty of analogical intuitions of various structures in four- and five-dimensional geometry. We can stereoscopically project or lay out the nets for or show some rotational sequences of geometrical structures whose dimensionality exceeds our direct intuition. This is particular (therefore intuitive, on the Kantian definition of the faculty of intuition) information about such structures, allowing us to differentiate such structures fairly well. But the asymptotic decrease in such analogical projection is such that an increasingly vague boundary between "knowable" and "unknowable" (on the Kantian model) spacetime systems appears: we can provide less and less intuitive descriptions of structures of higher and higher dimensionality, so our possible intuitive evidence for propositions involving those dimensions is reliably decreasing in scope, the more dimensions we assert in our theory. In other words, if all we need to explain can be done in a lower-dimensional model vs. a higher-dimensional one, that is to be preferred. But we take it from experience that what we need to explain might indeed require a few (so to speak) extra dimensions---for space or time (see Itzhak Bar's "2D time theory" for a decent example of the latter case).
Kant doesn't speak of analogical intuitions as such, but they are suggested by his remark about the terms of causation (this is in the section on the analogies of experience):
But in philosophy, analogy is not the equality of two quantitative but of two qualitative relations. In this case, from three given terms, I can give a priori and cognize the relation to a fourth member, but not this fourth term itself, although I certainly possess a rule to guide me in the search for this fourth term in experience, and a mark to assist me in discovering it.
So a 4-dimensional geometrical structure, for example, can be thought of as a fourth term, that by various distinguishing geometrical projections can be related to 3-dimensional space such that the principle of the analogies of experience allows us to "believe in" the 4-dimensional structure, if we need to believe in it (so to speak) in our best mathematical theory (supposing, which is contentious, that there is, after all, such a "best" theory).