Well, adjusting the sub trim in the AVR or raising the gain level in the sub both accomplish the same thing, but here is why you might want to use the AVR trim level:
Gain knobs on most subs are analog, and are usually quite sensitive. So, if you turn the gain up and don't like the results, it is difficult to return the gain setting to its exact original setting. In the AVR, the trim settings are digital. If you raise the trim 5dB, and subsequently lower the trim by 5dB, you know you are exactly back where you started. This may or not be important to you. However, if you use a room correction system like Audyssey, and trust the settings that Audyssey establishes, you always want to be able to return to the original settings after experimenting. Just my opinion.