This is an interesting question. I don't know if it's answerable in a very strict sense, and this is also why you might see alot of comments. This is basically another one, which got too long.
Firstly, username Yrogirg makes some good points in that many mathematical theories which are modeled using the set of reals (and I think I even used these terms in the technical sense here) entail many facettes which are really agebraic in nature. You can easily implement derivations by representing the quantities of interest as distinct symbols and translating the associated abstract rules of computation to manipulation of these symbols.
You formulate the physical problem and then its sulution by taking a look at the structure of the theory and you deduce the way to get from the object "boundary/starting conditions" $\mathcal{B}$ to the object "expectation value of observable" $\langle A \rangle$ (and stating the boundary for the system is also really only providing input which has been taken from another observable). Everything in between $\mathcal{B}\rightarrow\langle A \rangle$ is computational in nature in the sense above, so in view of your question one probably only has to bother about the real-ness of the objects on the left and the right. Measuring is fundamentally about comparing two things and as the rationals $q=\frac{n}{m}$ lie dense in the reals and so no human can tell the difference, I see no reason to be worried.
The same point is made if I say that if you define a curve to be perfectly smooth in the mathematical sense and then draw a picture of it by successively approximating it using finite lines. The experiment distinguishablity of the real and the approximated curve, for each level of sophistication, can be overcome by enough time and data storage.
The point you raise regarding the null-measure of the reals is not a problem as, with respect to the observables, I don't see why you'd need to manually integrate over points. Again, the numbers express or store information about a comparison. You might for example compare areas (how often does the first fit into the second?) or shades of gray (what is darker/makes the measuring device react stronger?), and if you "compare points" you really express distances, which means you'll compare lengths. Here you get into the whole unit business.
As a remark, although I think it's not very welcomed on this site, there actually are some papers (in subfields, in which some peolpe with names are involed too) which contain statements like
"What is needed is a formalism that is (i) free of prima facie prejudices about the nature
of the values of physical quantities—in particular, there should be no fundamental
use of the real or complex numbers..."
To sum it up, I think your first sentence "Almost every physical equation I can think of is expressed assuming continuous domains at least for one variable to range over" is exactly what it is. A method of representation. The method of getting at the results is implied by the mathematical relations associated with the symbols.
I personally don't take anything in physical theory particularly literally, but it's a useful and accessible language in any case, so that doesn't really influence how you do physics.