I kind of get why Hermitian operators here makes sense, but then we apply the measurement and the system collapses to one of its eigenfunctions. Why?
If I understand what you mean, this is a consequence of what we defined as a measurement (or what’s sometimes called a pre-measurement). Taking the tensor product structure and density matrix formalism as a given, if the interesting subsystem starts in a pure state, the unitary measurement structure implies that the reduced state of the interesting subsystem will generally be a mixed state after measurement. You might find parts of this review informative; it covers pre-measurements and also weak measurements, and in particular talks about how to actually implement measurements with an interaction Hamiltonian.
If I understand what you mean, this is a consequence of what we defined as a measurement (or what’s sometimes called a pre-measurement). Taking the tensor product structure and density matrix formalism as a given, if the interesting subsystem starts in a pure state, the unitary measurement structure implies that the reduced state of the interesting subsystem will generally be a mixed state after measurement. You might find parts of this review informative; it covers pre-measurements and also weak measurements, and in particular talks about how to actually implement measurements with an interaction Hamiltonian.