It depends, really. Obviously if you need to bring something in order to check something, then this is understandable. But take for example Landorus-I in OU. Its only two checks were Mega-Latias and Cresellia. This required you to either a) Use up your mega spot for this single Pokemon (while other megas could be considered better for most teams), or b), Bring a Pokemon from from a different tier just to take this single Pokemon on. Do you really think people really want to bring Cresselia or Mega Latias on their teams for a single Pokemon? Cresselia is easily outclassed by other OU walls (hence why it's in UU), and Mega Latias (while good) forces you to use up your mega slot.With that being said, I've noticed one of the most stupid and annoying traits on some of the past posts. People are complaining about having to run a check for something. God did you really have to make an adjustment to your team to meet the meta's new standards?I'm so sorry man!
But, as you said, in some cases this argument simply does not work. For example, if a Pokemon forced you to use either Mega-Metagross, Chansey, or Heatran on your team, then this is different because those three Pokemon actually have their usage outside of being checks for Pokemon.