Sadly, these contracts appear to be following the law of the land because our laws involving employment are trash.
The US minimum tipped wage is $2.13, with the other $5.12 necessary to meet the $7.25 minimum to come from tips. While the company is required to make up the difference, it isn't hard for tips to meet that minimum. Some locations probably don't make up the difference like they should, but the headline is based on the fact that Waffle House operates where the states use the federal minimum.
Like non-disclosure agreements and a bunch of other workplace shenanigans, it seems ridiculous that contracts that have clauses like this but they tend to do it because they have not been invalidated in court. Basically, you can put anything in a contract and the worst that can happen is a judge says "lol, no" because our legal system is stupid and has no protections against malicious contracts.
And the line for what is related work (like a bartender washing glasses) and non-related (cleaning bathrooms) combined with how contracts are legal until they aren't means it is possible the judge could rule in Waffle House's favor.
And no, it is not unusual for restaurants to have waitstaff do things that don't fall into the tipped category. They even point that out in the article.
A ton of employment issues like this could be solved by raising the minimum wage and getting rid of tipping culture.