Is it okay to use an LFNC whip to connect air conditioner where subject to physical damage?
This would be a decision left up to the inspector, as only they can say what's "subject to physical damage". Though technically, you're correct. Liquid-tight non-flexible conduit should probably not be used in these situations.

It's possible that the units come with the whip factory installed, so the HVAC techs simply install it that way. In my experience, the HVAC community doesn't always follow NEC very closely.