"Doch es kommt ja nicht nur auf das Innere an."
"Doch" means "but" in this sentence, so it does have a "real" meaning here.
By contrast, "ja" is used as a modal particle in this sentence. Modal particles are words that have been emptied of their "real" meaning (in this case ja = "yes") and are instead used to give some information about the speaker's attitude. They are used a lot in spoken German. Their meaning varies and it can be difficult to pin it down sometimes. In this sentence, I'd say the "ja" means something like "as I'm sure you know" or "obviously".
Since modal particles don't really exist in English, they are very difficult to translate. I think it's sometimes better to just omit them. Interestingly, however, there is one modal particle that is used in American English: "C'mon already!". AFAIK, the word already in this sentence is a loan translation from Yiddish "shoyn" (cf. German "schon"). Like the Yiddish/German modal particle, it has been emptied of its "real" meaning and instead conveys the speaker's attitude (impatience, urgency).
For more information on modal particles in German, see: http://coerll.utexas.edu/gg/gr/mis_04.html
Thank you. I am really wrestling with the idea of modal particles. They seem to be something like emoticons used in e-mail, though of course more complex and nuanced. I'm toying with the idea that emoticons have emerged precisely because we do not have model particles in English, or very few.