I'm really not a fan of these types of battles at all if they are absolutely unwinnable. I feel that if the player is taken to a battle in which they are in control, they should be able to win the battle in some sense, even if it requires massive grinding or absolute mastery of the battle system to do so. I also feel that if they win it should be acknowledged that they did in some form, be it a special item or just the cutscene after the battle changing a bit.
I have two instances that call for the characters to be defeated in the story in my own game. In the first, the story requires that the party be knocked out and captured, and there is a battle to facilitate that. If you just rush to the story events you'll probably be nearly one shotted, but if you take the time to do the available sidequests in order to get exp and equipment, you can win the battle. Doing so nets you a special item and a good chunk of exp (if you lose you get a not as good consolation prize later, and the good item is otherwise available later in the game). If you lose the fight, the party is unconscious on the ground when you return to the map and the scene proceeds. If you win, the villain is forced to use a special attack in the cutscene (my game is somewhat tongue-in-cheek, so the trope is acknowledged). The attack they use is actually a hint at a later plot point involving their character, so it's a bit of a bonus there too. After that, the scene proceeds in the same way with only minor alterations to the text.
The second battle, the boss doesn't even attack, and after a bit a cutscene ends the battle. If you deal enough damage to the boss before the cutscene triggers, you get some extra dialogue.
I feel that at least adding little touches to these encounters that allow the player some sort of "victory" makes them much easier to swallow. I know that as a player myself, battles where you simply cannot do anything except die horribly (especially the ones that would be easily winnable except for the fact that the boss has infinite HP... I am looking at you, Tiga...) really put a sour taste in my mouth. I'm more lenient if they occur near the beginning of the game, but if they happen at a point where I have spent significant time learning the game and building up my characters it really just feels like a slap in the face to me as a player. If you just want a sequence where the villain absolutely crushes the party and want to give no concessions, I'd much rather just have it happen in a cutscene that is out of the player's control.