This answers my question (you replied to it in the original place too). Thank you. I get the point you're making. And I can see how it's a bad system. Now that I think about it, I remember a similar problem with _ei? Sometimes it's pronounced <schwa>i and sometimes <a as in day>i. Yes, I also completely agree that Pinyin seems like a shitty system and very non-uniform system given what it set out to do and what it already had to take inspiration from.
That having said, the I still don't get the point you make about tone-sandhis and such. How do you propose they be incorporated?