Earlier quoted context omitted.
I don't understand Bengali at all. I'm trying to understand your second sentence though. When you say "no one writes that way", do you mean nobody hits the keys for letter, followed by vowel-silencing diacritic, followed by another vowel? Or do you mean the glyph that results from that combination of keystrokes doesn't match how a Bengali speaker would write it on paper? If it's the latter, isn't that an issue for th…
It has to do with how the text is rendered. For example, if you see the Bengali text on page 3 of this PDF: http://www.unicode.org/L2/L2004/04252-khanda-ta-review.pdf it is unreadable and incorrect Bengali. ;-)
To me it sounds like the rendering needs to be fixed, not Unicode.