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‘Yeah, well, the more the better,’ said Moody darkly. ‘We're your guard, Potter.’

‘We're just waiting for the signal to tell us it's safe to set off,’
said Lupin, glancing out of the kitchen window. ‘We've got about
fifteen minutes.’

‘Very clean, aren't they, these Muggles?’ said the witch called Tonks, who was looking around the kitchen with great interest. ‘My dad's Muggle-born and he's a right old slob. I suppose it varies, just like with wizards?’

‘Er—yeah,’ said Harry. ‘Look'—he turned back to Lupin—'what's going on, I haven't heard anything from anyone, what's Vol—?’

Several of the witches and wizards made odd hissing noises; Dedalus
Diggle dropped his hat again, and Moody growled, ‘Shut up!’

_{Harry Potter and the Order of the Phoenix}

"it" in "I suppose it varies" probably refers to "kitchen" in this context. But I don't understand "just like with wizards". Any thoughts?

"It" in this case refers to the trait of neatness/messiness. Tonks had originally assumed, based on her exposure to Muggles through her father, that Muggles in general are messy. When faced with the neat Dursley kitchen, her assumption was challenged. She then realized that it had been a mistake to generalize from her experience to all Muggles. She thus suggests that the trait of neatness/messiness might vary amongst Muggles just like the trait could vary among wizards.

In other words, "I suppose it varies" reflects Tonks's changing view of Muggle neatness/messiness. She had originally thought that Muggles are necessarily messy; she now comes to the conclusion that the fact that some Muggles are messy does not preclude the possibility that other Muggles are neat.

it will often refer vaguely to the current topic of discussion, to an idea or notion or fact, or to a situation whether at hand or being talked about. The reference will not always be to a specific noun earlier in the sentence, as you have supposed, like kitchen.

Some Muggles are slobs, and some are neat—it varies, just as it does with wizards.