The reason for not disturbing the sediment is primarily to leave the beer clear. If you are not concerned with keeping the beer clear because, for example, you drink it from the bottle, then disturbing the sediment does not matter too much. One exception I would say is bottled conditioned beers with LOTS of sediment such as a lot of home brews are. In these cases I think the sediment you get may be too 'lumpy' to enjoy. The flavour should not be affected in either case.

Cheers (hic)

Dave