Oh sorry. The yes was the answer to your question, and what followed was the explanation. How could speaking incorrectly not be a barrier to being understood? Am I missing something?

I'm not one of those linguists who has absolutely no interest in learning the language he's asking questions about, so I'm not sure if this is just some kind of abstract thought experiment, or what. Maybe you should make a recording of somebody speaking like that and ask native speakers if they understand it.

It would probably depend on how accustomed the Japanese speaker was to hearing their language spoken with a crippling, illogical English accent, which would really depend on their personal experiences. Since you admitted that people learning Japanese use Hepburn to read and pronounce sounds, I'd say it's unlikely that anybody has much experience hearing Japanese spoken like Kunrei realized in an English accent.

If you had the slightest interest in learning Japanese you might be able to figure out what you want to know based on the answers you've already gotten. I'm not even sure the "sh" in "shi" and the "s" in "si" as pronounced by an English speaker ARE allophones, because they seem to have minimal pairs. Otherwise, why would we need "sha sho shu" and "cha cho chu" as separate syllables?