Yes, some dyslexis like myself do. For example Pin and Pen both sound the same to me. I don't care how you try to pronounce them or with different accents. They are always the same.

What if the vowel sounds are isolated and elongated: iiii, eeee. Does that sound the same?

If someone is using the wah-wah pedal with an electric guitar to change the timbre of a note, can you tell?

Is it really about sound? Or is it just that the "phonetic analyzer" isn't distinguishing the phonemes?

If you can consciously hear the acoustic difference in timbre, how can you then not use that to tell the words apart (even if slowly/inefficiently)? As in "I just heard something that may be pin or pen; now I have to concentrate on what I heard. Hmm, the vowel sounded like a band filter tuned toward a higher frequency so it must be pin, rather than pen."

You mean like the letter sounds E and I. They sound different. I checked that with https://www.youtube.com/watch?v=SekEr_e3oaM - Yes I can. I think it phonic not sonic. I think it where the brain crosses the sound over the to concept of a letter or word. When I try to reproduce what it sounds like to be it comes out pin and pan or pen and pee-n.