I know you're not supposed to have them in the same deck flavorwise, but for more varied decks and possibly a healthier environment, is it possible for decks to have Orcs and High Elves. (I think those are two opposing factions.)

Is there anything in the rulebook besides one line that prohibits this? Or can you use both and I'm just a newb to the game?

The one line in the rules that says you can't mix Order and Destruction is all it takes. But for casual play, you're of course free to do as you wish. Opens the door to some serious unbalancing though.

Could you imagine High Elves with Skaven? HE have 2 decent restoration cards so you could corrupt yourselves all day long and be none the worse for wear.

Well, I have never played it a tournament or actually played the game. I'm in the process of getting the cards.

It's just in the "instruction" video on the site, they said you couldn't. And I thought that was fine flavorwise, but it seems like it just unintentional voids so many different decks that could change the metagame of professional tournaments.

Just something that I was wondering.

Are there professional tournaments? I've never heard of anything for money.

Well, not for money. But I meant "organized play" instead of professional.

I just don't necessarily see why the Order or Destruction need to be played separately. I think there is a line where flavor disrupts functionality, and this seems like it could be crossing it.

It's not allowed. It states as much in the rules. you are free to do it as you please in your play group.