Alexis replaced Messi when he was out. It's not about Barca's system, it's about not being used as a target man.
A 5 ft 8 Vargas is a fairly small guy too; and certainly less physical than Alexis Sanchez. He's hardly the towering centreforward who creates space for Alexis that you make him out to be. Chile play without a target man. If Alexis can play in a two-man attack like that he can play on his own too.
Again, I'm not advocating for us to just swap Giroud with Alexis. We need a better gameplan. Our game falls apart without Giroud because we've built the team that way, but the way we've built the team is not something to be proud of. We were moving away from it towards the end of the season, a fact that influenced Giroud's poor form just as much as fatigue. He can't make runs in behind the defence because he has zero pace. People want to give Walcott a shot up front all the time, but Alexis is a more natural striker in most aspects.