As a first-year ordinary Maths student, you take four courses each term, eight in total. They are:
> Michaelmas (Autumn term): Vectors & Matrices, Groups, Differential Equations and Numbers & Sets
> Lent (Spring term): Vector Calculus, Analysis, Probability and Dynamics & Relativity
Easter term is kept for revision and exams.
As a first-year Natural Sciences student, you also take four modules each term (but they are the same for both terms). They could, for example, be Physics, Chemistry, Earth Sciences and Maths. It is mandatory to take a Maths option.
If you take Maths with Physics, you take three of the four courses each term that the other Maths students take and the Physics course from Natural Science. So you would take:
> Michaelmas (Autumn term): Vectors & Matrices, Groups, Differential Equations and the Physics part of Natural Sciences
> Lent (Spring term): Vector Calculus, Analysis, Probability and the Physics part of Natural Sciences
At the end of your first year, you have two options:
1) Carry on with Maths: At this point you are indistinguishable from the other Maths students and the fact that you have done Maths with Physics is irrelevant. You get a Maths degree, just like the other mathmos.
2) Carry on with Physics within Natural Science: Generally, you are just like any other Physicist from the Natural Science course except you have less choice as to your later years' modules, which makes sense as you haven't done any of the other ones except Physics. You get a Physics degree, just like the other Natural Scientists.
You are not expected to know for certain which option you would like to take at the point you apply. This comes much later when you're already a student.
That is to say, Maths with Physics only affects your first year. The reason it does not come up as a unique course is because you apply to it as a Maths student. You would select it as an option just after applying but before interviews. You would be expected to meet the academic conditions of a Maths student, including meeting STEP conditions.
Side note: The distinction between pure and applied maths is very different at university level than at A-Level. Most of the A-Level Maths "Pure" you learn is actually applied at university. I must admit, I find their misuse of the term really confusing. It is something to be aware of.
Edit: You can see on page 7 of
https://www.undergraduate.study.cam.ac.uk/files/publications/my-cambridge-application-home-students.pdf the form that you would fill in from which you select either Mathematics or Mathematics with Physics