If metaphysical naturalism is true, would that mean that Physics is the ultimate discipline that can sufficiently explain everything, and that all other disciplines, including Chemistry, Biology, Cosmology, Geology, Neuroscience, Psychology, Sociology, etc., are just using convenient high-level abstractions/models/approximations that can be traced back and reduced to low-level primitives studied by Physics?
According to metaphysical naturalism, all matter and their interactions are ultimately a result of the interactions of their material parts (down to atomic particles and such).
Even for most who reject metaphysical naturalism, they still accept to a large degree the idea of that matter can be broken down to its composite physical parts (and specifically down to atomic particles).
For example, it's commonly accepted that the sensation of pain can be reduced to sensory receptors sending signals to our brains via nerve fibres (and then some stuff happening in the brain). Viruses and their interaction with various cells in the body causes disease. We can further break down the physical makeup of these things. It's commonly accepted that matter ultimately consists of atomic particles. When we "touch" something, this is actually electrons repelling one another. And so on.
Where non-naturalists deviate tends to be when it comes to the brain/consciousness and the origins of the universe. I haven't heard notable rejections of the idea that matter consists of atomic particles.
That said, when each person consists of around 7*1027 atoms, you can't plausibly model human-human interactions on an atomic level. The abstractions we use are a little more than convenient, they're necessary, for us to be able to say anything meaningful about the interactions of complex physical objects.
We could say there is weak emergence, which means more complex behaviours can emerge when combining simpler parts, but this can ultimately still be broken down into the component parts.
No, because of emergence. Saying other sciences are reducible to physics, is like saying literature is reducible to the alphabet.
What did emerge, Earth biology, didn't have to be that way, & the specific nature of a human in a society making sense of it's subjectivity, cannot meaningfully be predicted from physics. See: Is it the job of physics to explain consciousness?
I would describe the process not as reduction of biology and neurology to physics, but as about getting our domains of concern to interface with a common language where they overlap, discussed here: Is the idea that "Everything is energy" even coherent?
In this answer are details of David Deutsch's attempt to work out the minimum set of domains we need, to form a kind of 'meaning-cosmology' that can account for where we find ourselves: Could a new method of understanding the universe be created? The TLDR is that as well as physics (specifically Many Worlds QM, for him), we need epistemology, evolution, and information theory. He has been working with others on Universal Constructor Theory, which aims to make the emergence of life and information more explicable.
Under metaphysical naturalism, does everything boil down to Physics?
Depending on one's definition 'boil down', not yes, not no, but partially so!
You have one answer that says other fields like chemistry reduce to physics, and one that says emergence prevents that. So, the middle ground is that chemistry partially reduces to physics. In fact, there's a discipline called physical chemistry that has a foot in both domains, which helps to highlight what is in chemistry that is not in physics. Reductions also needn't be strictly hierarchical. Biophysics is a topic that looks at biological principles rooted in physics and isn't as concerned with reduction to biochemistry. What might be helpful to understand is that when we talk about reductionism in a domain, for instance, reductionism in biology (SEP), we can talk about both theoretical and explanatory reduction.
In psychology, we have the experience of heat. Our minds are capable of detecting heat. What is heat? A magical force? Nope. Heat is the psychological manifestation of the biological perception of a concept in thermodynamics, that of statistical kinetic energy of molecules. The famous philosopher Quine talked about 'webs of belief' which is a phrase that invokes the concept of confirmation holism. From WP:
In philosophy of science, confirmation holism, also called epistemological holism, is the view that no individual statement can be confirmed or disconfirmed by an empirical test, but rather that only a set of statements (a whole theory) can be so. It is attributed to Willard Van Orman Quine who motivated his holism through extending Pierre Duhem's problem of underdetermination in physical theory to all knowledge claims.
Thus, it might be best to understand the ambiguous phrase "everything boils down to physics" as the implication that a highly complex set of beliefs and knowledge does seem to have a direction that links together a web of belief such that certain ideas reduce as explanations and theories to others. The mind is studied by psychological principles which are rooted in the biology of the brain which is built out of chemicals which are understood in terms of atoms, and so on. Is pain an atom? No. So pain doesn't reduce to an atom, but through a series of claims, it can be shown that pain can be explained in terms of atoms ultimately.
If you want a great introduction to this sort of topic, consider reading Consilience: The Unity of Knowledge by Edward O. Wilson. From WP:
Consilience: The Unity of Knowledge is a 1998 book by the biologist E. O. Wilson, in which the author discusses methods that have been used to unite the sciences and might in the future unite them with the humanities... Wilson uses the term consilience to describe the synthesis of knowledge from different specialized fields of human endeavor.