Players don’t have a choice to use gestalt or not
Gestalt is something the DM chooses, as the rules for the game. So as a player, you’re either playing in a gestalt game, and thus must use those rules, or you are playing in a non-gestalt game, and cannot use those rules. Aside from looking for a gestalt game to play in, the player has no ability to choose to use gestalt.
This is consistent with Unearthed Arcana as a whole. Other supplements, like Complete Arcane or Tome of Battle, provide additional rules that are simply added on to the existing game. If the DM says those books are in-play, you can use the options in them; those options are just supposed to fit into the game without a problem. Unearthed Arcana is different—the DM can’t just say it’s “in play,” that doesn’t make any sense. That’s because rather than add-on rules, Unearthed Arcana offers a bunch of variant rules—they change how the game is played in fundamental ways. The DM has to decide which variants they are or are not using. Many variants simply can’t be used at the same time as others.
Anyway yes, gestalt characters are stronger than non-gestalt characters. It’s far superior to regular multiclassing. That’s an intended and understood aspect of the variant—and Unearthed Arcana goes out of its way to warn DMs about that. A DM has to make challenges harder for gestalt characters than they would for non-gestalt characters of the same level, because a gestalt character has more abilities and features than a non-gestalt one. In one game I’m playing in, our characters are 6th level, but have four “layers” of gestalt (that is, two more after the usual second one for gestalt)—we are routinely fighting challenges intended for characters in the mid-teens, because even though we’re still 6th level, all those features make our characters fairly powerful.