The LLVM IR is a representation of the C Source Code. But the constraints generated for the statement in C and in IR might be different.
For example, p = *q; is a single constraint of Deref/Load type in C, but results in two Load constraints and one Store constraint in IR.
But this doesn’t mean that the result of performing the points-to analysis on C source code is different from performing it on the IR!!! In IR, you just have a more finer view into the memory operations, but eventually, the points-to sets for a memory location / variable will be the same whether you do it in C or LLVM IR.