I think what they're saying is that each substitution is to be treated as a kind of stand alone event. So Villa doesn't play and is replaced in a team, 4-4-2, with Miguel.
In a separate event Xavi doesn't play and is replaced in a 4-3-3 team with Campanero. So Miguel and Campanero don't actually play in the same team. Kind of thing.
I think this is actually the easiest and fairest way to use the subs. So why they've chosen to write the rules in a way that makes it look like it works in a totally different and more complicated way I don't know
I don't know this for sure, I'm just guessing going on what they've written. To be honest this format is so weird I've never bothered checking scores, I don't even know the rules, I just try and get 11 on the pitch each week with a decent captain and hope for the best.