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 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?
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.
Full literacy in alphabetic-phonetic languages includes the steps of (1) no longer sounding out words aloud and (2) no longer sounding out most words in your head, but rather grasping the shape of the word immediately.
I suspect those involved in programming skew very much towards the word-as-symbol, but whether that is causative or correlative I can't say.
Interestingly, perhaps, is that I recently made the transition from word-as-sound to word-as-symbol in another language - morse code; that felt very odd while it was going on - I have parsed words character by character for a couple of decades, and suddenly, I found my decoding lagging further behind - I had started hearing words as units, rather than composites of characters. Funnily enough, it was through no conscious effort - just happened, over the course of a few hours.
I think I've read somewhere that reading is basically done by the brain registering the first and last few letters in a word, then just checking whether the ones in the middle are more or less what you expect and where you'd expect them. (In other words - if the start and/or end of a word is altered, your reading speed and comprehension should take a nosedive compared to just messing with the letters in the middle)
If there is some truth to that, it would go a long way towards explaining why we can read it with as little trouble as we do.