That is all fair, if it were a CFP committee I think you are right, they are probably looking at multiple variables.
I think that outside Valpo's games vs CP and Penn, the next best game is Merrillville, which is a tough game, but the rest of the conference isnt very good. Andrean being down this year didn't help.
Snider overall has two quality wins vs 6A teams, yes Warren did not live up to their normal expectations, but Carroll was a very good 6A team. I think Snider would likely take the overall #1 spot, but the loss to Homestead is big hurdle to look past.
I like the Snider v Merrillville matchup you have in your final 4.