For example why does rabies start it’s replication process in the pons and not anywhere else?
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There’s a significant difference between the different cells in your body and bacteria and viruses have a very hard time being adapted to all of them at once.
Your nerve cells don’t replicate at all while your stomach lining rapidly replicates to maintain a barrier with the highly acidic stomach acids. While most bodily fluids tend to be neutral or slightly acidic your intestine is usually basic, etc.
Immune responses also tend to vary a lot by region, I’d the skin is broken there’s a risk of bacteria entering the bloodstream directly and ass losing a little bit of skin isn’t live threatening the immune system can be relatively aggressive, but certain areas are ‘immune privileged’ which means the immune system isn’t as effective for fear of damaging structures important for survival (the brain and eyes are one example). But those areas are usually protected in other ways (the blood brain barrier helps to keep pathogens out and the skull usually prevents wounds from directly depositing pathogens in the brain) so they can be hard to enter.
One pathogen might be able to invade the lungs, but would be damaged too much by the stomach acids, another one might have the ability to withstand acidic conditions but be unable to overwhelm the immune system while in a wound.
While eating an animal infected with rabies is highly discouraged the likelihood of actually contracting disease is actually quite low since cooking and even just digesting the food usually destroys the virus(I’d still not recommend it, because rabies is incurable so if you get unlucky that’s it).
TLDR: different parts of the body are different and pose wildly different challenges to pathogens, no single disease can master all of them, the same way no single jacket will work both in dessert and the arctic, different environments need different solutions.
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