The problem, especially with small breweries, is often technological. If a small brewery cannot afford a fancy bottling line they will often have cheaper bottling lines with a lot of manual involvement. A lot of small breweries that bottle 22 oz. bottles, for instance, use 4 row bottlers that require a person to use a device to shoot CO2 into the bottle, to ove the bottle over (exposing it to oxygen) and to place it onto the machine, which has a precarious sealing mechanism. Then, the brewer has to try to cap on foam so some small brewers will place the bottle under a bench capper (hand one) and then tap the base of the bottle with a screwdriver handle or something until the bottle foams. then they try to cap on the foam, which hopefully, has pushed all of the CO2 out. While this won't necessarily change the substantive nature of the beer, when you introduce oxygen, and dust, and other external elements the beer may be exposed to, you won't have the same product consistently. Kegging is much easier to do with cheap equipment and doesn't have any oxygen exposure issues due to the pressurized nature of the keg. It will often be done in the cold box too, instead of on the floor, so there is no risk of the beer warming as it travels through tap-like lines and thus losing some CO2 with the rising temperature. The part about the brewery using different hops is a whole different type of problem and would be a surprisingly stupid thing to do IMO.