The game starts with a handshake, an unwriten rule thats in place for centuries, and has recently been added to FIDE rules (not he handshake itself, but refusal of handshake).

So how can the game begin if one of the players isn’t there???

The point is chess is a turn-base strategy/tactics game, not a real time contact sport! You don’t have to wait for your opponent at all, you make your move and push the clock, or the arbiter pushes your opponents clock, and his/her time is running, while you can score a drink (or a smoke for that matter, but as we all know it not only costs points, but also kills…) In chess there is no running against the chronometer, nor any goals to score or balls in a zone the opponent has to defend! In short, there is no need whatsoever for both players to be present at the board all the time, and not even at the start of the game. We all know that, but FIDE hates it because IOC members have no clue about this, and just consider it “unprofessional”. And of course, IOC is where the real money is and that makes all the FIDE bigshots drool with greed, so that the sold out our game in vain hopes of Olympic status. Ha ha, that will never happen…!

If the rule is bad, then what are the suggestions, how long should the opponent wait for her/his late opponent?

OK, you (like many other) don’t like the rule. BTW, one should distinguish between wanting some tolerance (one hour was the standard ’til recenly) and no limit at all, supposedly letting the chess clock be the only ruler on time, for the game. (On this last case, it seems there still is some incoherence, and people should also be against that rulling!).
The most dificult point in discusion here wasn’t exactly that, but OK, I too have an opinion.
As you rightly pointed, there is a question of “politeness” (and rightness, I’d say) in being on time (or not) to a scheduled event.
For instance, I say one player having arrived to his game should NEVER be harmed in any way by the absense of his opponent. Even if he is playing White, he should never have the onus of making a move in order to have his absent opponent’s clock running. EVER! (That’s a rule I’m against to).
As for the “new” rule itself: It is only new in establishing some different tolerances. It is not a hour anymore and, in FIDE tournaments, it is zero tolerance.
My opinion is that it is OK.
First, it allows tournament organizations to put a tolerance they find suitable, the main thing being everybody knows it and everybody entering the tournament ACCEPTS it. And 2nd, even when the tolerance is “zero”, all you have to do is REALY try to be on time — even being some time before, if needed! Just like when catching a train or a plain. I lost games for far more stupid rules! This one is gold, for me, in comparison.
This rule was not one of the most needed changes, but Well done, FIDE. (Though the “old” rule was acceptable too. It just had the guillotine exactly established at one hour. The “new” rule simply grants more freedom.)
There’s no problem in protesting against a rule, if you don’t agree.
The problem is lots of people behaving as if they didn’t know, if they know but expect it not to be aplied, or as if this particular rule is a great injustice, or even illegal! It is not illegal nor great injustice, but even if it was, the desire should be knowing rules are equally aplied, and until the unfair ones be changed (and the “illegal” overulled).
You ask:
“who benefits from two great players being knocked out of the tournament?”
I answer “Everybody”!
Not because I’m sort of a “rules and laws addited”, but because that sad event (BTW exclusively caused by those players absense, with more or less blame on them) MUST not be easy to happen again, and because it is that way for everybody, and because it is not sadder than if the tolerance would be different but also broken by the same players.
And yes, on this case we even now know they have been warned and called to play 5 minutes and then 1 minute before.
I wish every FIDE rule to be as problematic as this one!

OK, lets say that there would be 5 minute tolerance ( a palyer can be 5 minutes late). What do you do when someone comes 5 minutes and 23 seconds late? That person should be forfeited because of those 23 seconds, right? If not, where is the limit?

And we are back at the beginning. It’s the same thing if there is a zero tolerance and someone comes 23 seconds late, or if there is a 5 minute tolerance and somebody comes 5 minutes and 23 seconds late. Completely the SAME thing. That person is going to get forfeited for those 23 seconds. And there would be ragging debates about stupid ruile that got him forfeited because of those 23 seconds.

The rule is just fine. Players weren’t in the playing hall when they should have been. Period.

My opinion on interpretattion of this rule in Hou Yifan’s case was a little bit different, because she was there in the playing hall, she just wasn’t sitting at the table. That decision to forfeit her was not in the spirit of the rules, but in this case it was perfectly OK.

One pushes the clock and the game starts. Who cares the opponent is unable to directly answer, because he is still away fetching coffee? Award a win by default for that? FIDE-logic and FIDE-justice.

Only 2 players are already sitting at the board.
Officials looking at them conspiratorially…