Whoever told you that was either misimfommed or they flat out lied.
Believe me...beneficial bacteria will grow on the liner just fine. Your filter should have plenty of beneficial bacteria in it also. Rock will trap all the fish crap and uneaten food and allow it to decay in your pond. This makes the fish's pond much the same thing as a toilet. The sludge that developes under those rocks provides a breeding ground for bacteria (not the good kind), parasites and allows hydrogen sulphide gas to develop (which is deadly). Additionally, koi can easily get scratched or cut on rocks and with that bacteria breeding there, their little wounds can get infected and lead to death. Rocks in a pond are BAD. A properly designed pond has no rocks in the bottom. There should also be a botom drain that carries all the waste to the filters.