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Seems to imply that 1000 calories of junk food (carbs) makes you fatter than 1000 calories of chicken (protein).

Is this true, or is the effect of the above small enough that it's biggest contribution to weight gain/loss is overeating?

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Yeah, the implications in that quote seem to be slightly wrong.

They're implying that eating too much sugar makes it get stored in fat, which makes you fat.

That's bad old pseudoscience sort of like "eating fat makes you fat" or "do low intensity cardio to burn more fat". The truth is that eating food and storing energy as fat does not mean you will be gaining fat. It's now widely established that short term fat burn or fat gain really has a very small affect on body composition and by far the dominating factor is just if you are running a caloric deficit or not.

On the other hand, in practice it basically is right. If you eat a lot of sugar, it will turn into fat and you will also lose energy because of the insulin spike, so you're unlikely to work out hard. Even if you do work out hard you may not be getting enough protein and may not have good muscle balance.

For example, two people who both burn 2500 calories and eat 2500 calories - neither will gain or lose any weight, but if one of them eats mostly simple carbs and the other eats mostly protein and veg, the latter will have a better muscle/fat ratio if they do the same exercise.

And of course as JR points out there are many health affects of food besides just weight gain/loss.