MTB-2 is very vague in saying that bronchoalveolar lavage is placing the bronchoscope into an area of lung normally not colonized by organisms.
The only thing I'm aware of is that it's placed distal relative to where a tracheal aspirate catheter would be placed.
Although a lavage would obviously lead to fluid flowing deeper into the lung before being recollected, that still doesn't answer the question as to where the bronchoscope is actually placed for a bronchoalveolar lavage.
Regarding the mucociliary clearance, my guess would be that we'd still see organisms along the epithelia despite the mucosa's attempt to clear them.