It's not a matter of better. They are different kinds of conditioning and somewhat different process. One, bottle conditioning is dependent on the activity of yeast and carbonation.
For big beers I leave them in primary for a month to finish fermenting (they tend to be slow anyway) and to let the yeast clean up, then I rack to a secondary for several months to bulk age before bottling. Bulk conditioning tends to be mellower, and it all happens together. Slight differences in temps of the bottles could cause slight differences in each bottles.
It may or may not change the timeframe of the final conditioning in the bottle, some things still need to have the co2 of carbonation to clean and mellow, so don't look at it as a way to speed anything up...look at it as a way to make great beer.
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