I believe she wouldn't be the champion based only on the fact that she didn't beat all the gym leaders to get the badges required to challenge "officially" the E4 and afterwards beating Ame. Also, on other games we've seen the champion going around with a "weak" team (except their ace) to try new talents, so beating them outside an official match would hardly be a qualifier to become Champion.
Are they with Team Meteor though? Taka is basically forced to play along with them due to his father and family's tradition (while he undermines them a lot, by helping the MC for example). And Lin is a blackmailed version of a fusion of 3 people (as we can see in the "lab" in Ametrine) with one being a kid, a second a blackmailed scientist and a merc who worked for meteor and (if I remember correctly) lost its faith with them and chose to split up and how to fix their bodies. They are a bit grey characters, but too "good" moraled for being bad guys.