Well, Jessie and James are in Yellow and LGPE, so I think it still stands. They just used a little loophole.
Unlike other characters that have made appearances in the anime (i.e. Iris, Clemont, etc.), Jessie and James in Pokemon Masters have their original anime voice actors.
Plus, Meowth actually speaks in Pokemon Masters as well, unlike in LGPE. Adding in the appearance of Shiny Celebi, I think, at the very least, even if TRio in Pokemon Masters are not the main anime version, they are still the M20/21/23 version.
Since they have opened the door for anime characters, I do hope they will consider manga characters as well. Red (Pokemon Special) with Venusaur, or Red (Pokemon Pocket Monsters) with Clefairy would be cool appearances! What would be other manga characters that everyone here would like to see?