I think many people do have brains that operate this way, probably because their understanding of language is grounded in conversation as a first experience. I suspect this is the reason you see confusion with "your, you're" and "there, their, they're."
I don't parse language in quite that manner, and even in speaking I have a different "mouth feel" for those homonyms. This creates a modest inversion of the idea of spelling errors for me, in that people who truly do say homonyms in such a way that to my hearing it is exactly the same require me to parse for context.
> I don't parse language in quite that manner, and even in speaking I have a different "mouth feel" for those homonyms.
I believe in the (somewhat controversial) non-subvocalization-based text processing and even think I do it myself, but I'm wondering if you could describe more about the "mouth feel" issue. Do you mean that you believe that you pronounce them using different phonology (that another person would potentially be able to hear), that your muscles are doing something different but not in a way that makes an auditory difference, or simply that you're subjectively aware of the spelling while speaking but not necessarily in a way that makes a physically-observable difference? Or is it not quite clear which of these is the case?
I think this is an interesting question in the philosophy of language and also in the psychology of reading. (I've thought about this myself but haven't studied the academic literature about it.) If your answer is the first one, I wonder if you'd be willing to make an audio recording of yourself pronouncing these words that might show what difference you experience.
By the way, there are documented cases where spelling differences have created new pronunciation differences that didn't previously exist in the spoken language. Maybe something like that has been happening in your idiolect?
I have a similar feeling, when I pronounce a homonym/homophone. The word "mouth feel" resonates for me, although I suspect that sometimes it's just an awareness of the spelling of the word. Other times, I'll consciously choose to pronounce a word differently to try to disambiguate it. I'll say "aunt" as "ant"/"ont" (read those second as phonetically-spelled Californian American pronunciations) depending on the situation and flow of the sentence. "They're" is usually "They-er", "their" is sometimes "thur" (like "fur" with a /ð/), and "there" feels like it's pronounced the expected way. "To" might be "tə", but "two" and "too" never are.
Of course, that's all when I'm paying close attention to what I say. I'm sure there are times that I go against those. Also, sorry for the mix of layman phonetic spelling and IPA.
I don't parse language in quite that manner, and even in speaking I have a different "mouth feel" for those homonyms. This creates a modest inversion of the idea of spelling errors for me, in that people who truly do say homonyms in such a way that to my hearing it is exactly the same require me to parse for context.