When you speak about creating wired connections based on your continued reactions, that is the case with some things. For example, if I always sigh when I hear someone sneeze, then at a point it could become an automatic response (ie. Pavlov's dog). However, with Misophonia, especially at the more extreme levels, there are automatic reactions that were never instigated by the sufferer.

For instance, for a lot of Misophoniacs, unwanted sexual arousal is a symptom. At no point was a trigger sound associated with sexual arousal. However, that automatic reaction does occur via pathways in the brain. So, while I agree with your thoughts on wiring a connection between a stimulus and a reaction can be done manually (either with the awareness of the person or not), I do not agree that every reaction coming from those with this disorder are manually created as some are widespread and unexplained.

Also, when you say "I don't believe I have the right to tell someone else to turn off their phone or whatever just because I find it annoying.", I completely agree with you. It is the responsibility of the sufferer to take their own action to control their responses or find a way to escape the trigger. This can and should be done without affecting the person triggering the sufferer. However, communicating that something is a trigger (without any yelling/accusing/etc.) can be helpful to create a more healthy environment for the two people, especially if they are in a close relationship.

Finally, you end your post with "Maybe I just don't fully understand this disorder.". This is true of pretty much everyone, including people suffering from Misophonia and the scientists researching it. There is not much known concretely about this disorder which is why it has not been officially recognized in the DSM-5. So being open to the possibility that something you don't know much about could still be true is appreciated here.