I'm not a syntactician, but I hypothesise...

The phrase "student of X" is a syntactic unit and cannot have any of its parts substituted. Thus the student of physics cannot become one of chemistry or student of it. Student of X must remain complete (of course, a different subject can be named, but neither student nor the subject can be substituted by a pronoun of some sort).

Jack met the student of physics and I met the student of chemistry.
*Jack met the student of physics and I met the one of chemistry.
*Jack met one student of physics and I met the other student of it.

However, using from means that "student from England" contains three units and each of the principal terms can be substituted.

Jack met the student from England and I met the one from France.
Jack met the student from England and I met the tutor from there.
Jack met a student from England and I met another from France.
etc.


Since this is a problem that vexes even the most serious linguists, I have only a suggestion to propose: that "one" in this construction can be a placeholder for something that functions as a definitive, single-option identifier within a category. In other words, it works for words where one modifier rules out some other modifiers.

If you're tall, you can't be short. If you're right, you can't be wrong. If something is smooth, it can't be rough.

Someone can be both a student of physics and of chemistry, without any confusion. But to say someone is from France and from England is ambiguous and somewhat off-putting. It makes it unclear where the person is originally from, or when they were "from" each place. In that sense, being from somewhere is a definitive trait.

On the other hand, being a student of chemistry is not definitive. One could be a student of chemistry, physics, and art history.

In this sense, it seems to me to be less a question of syntax than of semantics. Consider that the second sentence could be rewritten with the objects of the prepositional phrases used as adjectives modifying the student.

Jack met the physics student and I met the chemistry student.

It would still sound unnatural to write:

Jack met the physics student and I met the chemistry one.

But why? It isn't a problem with other phrases of identical construction.

Sally ate the red popsicle and I ate the blue one.

Jim was the right man, and Tom was the wrong one.

Being red or blue are likewise definitive, single-option traits. They describe the object in a way that clearly divides the two options into discrete possibilities. Because the options are clearly distinct, replacement with a pronoun is more natural.