Th epronounciation of the words has nothing to d with the actual letters in pinyin. The idea is a system, an standarization we all agree with. It is a representation, not meant to be representing the actual sounds in teh same way a Chinese character tells you nothing about the pronounciation. You learn to read it according to conventions, and those conventions in teh case of hanyu pinyin are the ones most widely known.The pinyin is not meant to be used by Taiwanese, but by foreigners, and the one more foreigners know nowadyas is hanyu pinyin. We can argue till we are blue in teh face of its faults, but that is a fact.
It is the same with the current problem of most "English" websites. They are written by Taiwanese to be enjoyed by their superiors, hence, no real actual useful information is provided. Therefore, business opportunities are lost, no one knows a thing about Taiwan outside of Taiwan, and if anyone looks at them, they think taiwanese are not professional.
For linguistic studies, there are several international standards in place, one most generally acepted is international phonetic system. To invent one and then push it is not practical. If one were to present a paper or dissertation at an international congress or prestigious house of higher learning abroad, one wants to be understood. To share knowledge is the goal. So it is reasonable to use an international convention, a system that is in existence and that most scholars would understand. That is the point, to be understood.
However as said, politics get into play and decisions are taken based on making a name. It is like Taiping Island, no matter how many times we call Abu Daba or whatever, that is not going to make it any much ours. As a matter of fact, it will discourage support as people will not know what the heck you are talking about.
We cannot make fetch happen.