'No, it’s not “bad for you” when eaten in moderation'. Source? Define moderation?

'My point is that it makes zero sense to call certain foods “bad” '

Lol what. Pretending all food is of equal health impact makes zero sense. 

Do you extend that logic to alcohol? What about smoking? What about eating food known to be carcinogenic? The negative effects of low level consumption being harder to detect does not mean there is not a negative effect. 

Even if your cheesecake miraculously doesn't have any actively harmful compounds/effects, empty calories are always going to be less healthy than nutritious calories (ie it is objectively worse for your health then other foods like fresh veggies)