I understand your point. As far as I'm aware all sports, worldwide, are played under the same set of rules. It seems to me fundamentally unfair if some players/teams are treated differently in the same competition. I suppose the rules could be varied from one competition to another provided there was no relationship between the two competitions. Even this is debatable.
If the rules vary within the competition all sorts of potential difficulties arise. I'll limit this to one possible scenario in the initial WC league stages. A v B is played at 40⁰ with hydration break, while C v D is played at 22⁰, no hydration break. Kick off times are the same. A v B will last six minutes longer than C v D.
Both A and B require only a draw to qualify for the knockout stages. C and D both have the possibility to qualify provided they win and either A or B is defeated. The match between C and D finishes six minutes earlier with a win for one side. At this point A v B is 0-0, a quick phone call tells both managers there teams have qualified at 0 - 0, there is no need to risk defeat and a draw is played out by "cooperation" between the two sides.
Yes, there can be other scenarios in which the games finish at different times but those are all influenced by the same set of rules. I've been at such a game. May 14th 1995 I was at Anfield. Rovers had lost 2 - 1. United were drawing 1 - 1 at Upton Park. The whole world knew Utd must score to become PL champions. Had Utd scored there could be no complaints, if that game took six minutes longer because of hydration breaks and Utd won there would be every reason to complain. Utd drew with WHU and Rovers were champions, had Utd won they would have been champions.
Two different games played under different rules in the same competition simply cannot be allowed.
Well if it's that much of a problem, just start the game that requires hydration breaks six minutes earlier than the one that doesn't 🤷♂️
You wouldn't pause a different game for any other reason if its parallel game was paused, would you? If a dog runs on a pitch and it takes four minutes to catch it, you wouldn't pause the other game for four minutes. A player needing ten minutes of treatment on the pitch? Delayed start due to turnstile issues or traffic? Betting syndicate unplugged the floodlights in the second half? The referee has ample opportunity to pause or delay a game already, this isn't really any different.
As for your example - if Man U had only needed a draw to become champions it might have worked. The fact they needed a win made it irrevelvant that it finished later. It's not like they would have been given six extra minutes to find a goal if they'd had a hydration break (we'll not get into a discussion of Fergietime here...)
Because what's really not fair is a team that's done the work to get the opposition on the back foot, that's pressing players that are disorganised, whose legs are burning with lactic acid, who are no longer sure if their gameplane is right and if they're making the right decisions, being told to stop playing for three minutes so everyone can have a break when it's only 23C and its absolutely unnecessary. Because so much of football is the attempt to engineer that exact situation. You know that total football stuff the Dutch played in the seventies (that is also foundational for Spanish tiki-taka, through Cruyff bringing some of its ideas to Barca)? Listen to e.g. Cruyff speak about it. Everyone loved it for being free flowing, but tactically it was about using possession of the ball and the technical ability to swap places to engineer numerical advantages on the pitch and make the opposition run more. Total football was
essentially about tiring the opposition out by using the ball and switching positions. Four quarters destroys that.