First, it's ROMAJI, not romaNji. Characters from Roma (rome), not characters from "Roman".
All romaji japanese words spelled in kana? I have no idea what you are saying. You can't "spell" romaji in kana, they're two different writing systems. Either it's kana, or romaji. All japanese words are spelled in kana (or kanji), romaji is just an APPROXIMATION of what it sounds/looks like using our writing system.
ALL kana charts are the same. Some include old kana that aren't in use nowadays, some don't, but they all have the same kana. The sounds are all the same. There can be variation depending on dialect and such (like the normal "g"/nasal "g" distinctions), but that's it. There is no pronounciation different between someone who decides to write the kana "しゃ" like "sha" or one who decides to write it like "sya". It doesn't matter, romaji doesn't determine pronunciation, it's the kana that does.
I bet Japanese people probably would love to do away with all that romaji silliness and have everyone use the proper writing system so there's no confusion.