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The comparison you brought up is completely different.That could just be an artstyle thing. You're not gonna tell me episode 51 of Pokemon BW is non canon to episode 32 because Ash looks shorter in 1 episode right?
This is Red when he was 10
This is red when he was 20
This is red in masters
Red in Masters is completely different from Sun & Moon red while extremely similar to his 10 yo self. This means that this could simply be red after his encounter with G&S trainers or his encounter with the BW2 trainers. Actually there do seem to be references to his mt. Silver showdown so yeah, this is simply post-gold, pre-bw red.
There's exactly 0 reason for him to go through a complete style change if they wanted to use 20 yo read, they could've used his Sun and Moon model which would've worked well. Additionally, no other character went through a "style-change", their old polished models are used. Ethan (who's barely any younger than red), Brandon, May, none got significant style changes despite the fact that by your logic they should've been way older.
This turns into the simple argument that the timeline of events is completely different here and thus it leaves the two pre-established logical conclusions
1. These characters are dragged in from different timelines, which would need support from the plot which is up to masters fans to prove.
and
2. The events don't happen in the mainline canon and thus masters is its own canon just like the anime and the manga.
Option one needs proof, if there is any at all, however the timelines argument denies there being more than one legendary since the pokemon of the trainers in question would be dragged in with them from different universes.
Option two is a basic and logical conclusion. An app game with pokemon trainers in the exact state as they were in their respective game not being canon to the main games makes absolute sense and if this wasn't pokemon but some other verse we wouldn't even be here arguing since everyone and their grandma would understand the fact that it ain't canon.