Ok to answer your question very carefully, of course as pilot in command you have the final authority as to whether to land the aircraft or not, just as you have the right to decline an LAHSO if you feel that your aircraft cannot safely come to a stop before the intersecting runway for example. So regardless of a clearance to land by the tower, if something doesn't feel right, you're not obliged to comply. I mean that's just the safest thing to do.
I have personaly never recieved a clearance to land when visually confirming that another aircraft or other obstruction was on the runway. I do know however that if travelling as a 'flight' with another aircraft, you may be allowed to land prior to the other aircraft clearing the active. I personally had to do this about a year ago. I believe that ATC have their specific distance requirements between aircrafts in such an example, however I can't recall the numbers off my head. Hopefully an air traffic controller can fill in this detail.
Hope I've helped some what...
