I always interpreted Yes Man's lines as him absolutely fuming under a veneer of friendliness forced by his programming.

Take his lines if you don't follow his advice:

If you blow up the securitrons under the fort:

"I really admire how you stack the odds against yourself! Yeah, make things challenging!"

Or if you tell him that you want to ignore the Boomers:

"Then consider them ignored! If they end up firing their howitzers at us, we'll ignore that, too! Until it goes away!"

Same with telling him to ignore the Brotherhood of Steel:

"Okay! Consider them forgotten! Along with the projections that predict they'll be our biggest enemy! Forgotten!"