does using the Hepburn standard of romanisation address the issues mentioned here or not?It does. Although don't use modified Hepburn. I don't think we want to start having to write things like よう as yô or yō.
I think this chart should be used as quick reference: http://www.library.illinois.edu/asx/jap ... table.html
while not completely relevant to this discussion, there are actually modern words that use ヲ in stylized spellings - ヲタ (wota, short form of otaku) comes to mind.Have you ever heard ヲタ read aloud? I haven't, but I also have never seen or heard a native Japanese speaker read ヲ or ゐ in their classical sense (hence why they are obsolete). Even when people like to use them in names of characters/works to make it seem fancy. Quick example would be Sora no [W]oto [ソ・ラ・ノ・ヲ・ト] (lit; sound of the sky) where in classical Japanese oto would have been spoken and written as woto (as with MANY words that use お). Usage of ヲ here is to make it seem old and interesting. It's also basically never romanized to Woto, since it's not read that way by modern standards.