I've never heard anyone say, "Iya sama-sama". Only "sama-sama".

Also - why is "iya" accepted on some as "Ya" and not on others..?

I write "iya, terima kasih" on another and it's accepted as alternative solution - not here.

Consistency required.

Iya is correct. It also helps differentiate (phonetically) from "Ja/Yes" in German and "Я/I" in Russian, for any polyglots - "ya" is a teenage girl from the USA who just started their freshman year trying to sound cool when they are, "ya, like, totally?".

More formally, can't you say "kembali" instead of "sama-sama." You don't have to say "terima kasih kembali" in full right?

This translation is wrong because it is out of context. The correct direct translation on "Yes, You are welcome." would be "Ya, terima kasih kembali." and not "sama-sama". "Sama-sama", translated and used on it's own, simply means "the same".