Yes and no.
It counts as a take-off and a landing and it counts as a dot/line on my maps. It also counts as BIS miles flown. But it doesn't count as a visit to the country/state/city where the stop happened. I recently flew ACC-ROB-BRU. I earnt FF credit for ACC-BRU and only one EQP but on my map it is two segments and all the miles. But I do not consider myself to have visited Liberia. Even had I deplaned and hung out in a transfers lounge I wouldn't have counted that.