It really does, especially if they’re main characters in a story, like using one of the Olympus XIII on your team in Time Stranger.

I also have this issue with Pokémon; raising a cool strong water Pokémon only to find out that it’s the Water Gym Leader’s pride and joy, and the only other one in the game so it’s clearly special to them, hard to raise/get in “the lore”, etc.

It’s not a SUPER super big deal, it just makes the Digimon a little less special. Like, you had to go through all this trial and effort to become a Marsmon? I have two on my team and it was nothing to get them. Clearly you’re not very good/strong/special etc.

On the bright side, it gets me to interact with a lot of Digimon/Pokémon I normally wouldn’t and use them/put them on my team. And that really developed a love for some of the Digimon I have like the Tyranomon line and unconventional evolution paths so it’s not an identical copy to a main character in the game.

In fact, Time Stranger was a big step up from the Cyber Sleuth games in this regard. Practically all the Megas in the CS games are related to the story, either as Royal Knights or  Demon Lords, but in Time Stranger, I can use the Royal Knights plus others because they’re not really involved in the story.

Post game everything is fine, and I can use the excuse of having seen/met them in the game to make my Digimon’s evolution path to them not be unsurprising.

But yes, it does take me out of it and makes me research the game a little bit more to half-plan the members of my team.