IMO the MB system is great as it is. As a Crafter I also encounter into a situation that I need 1 item of a 99 stack, and as a Gatherer I want to allocate my retainer slots to sell various items as possible as stacks of 99 for profit.

Gil vs. Time:
As a Crafter I learned that as you level up, you sell more & "normally" you should start buying more. Both I (Crafter) & Seller (Gatherer/Looter) are benefited; the MB System is designed to rotate gil in such way! Otherwise if you want to be Jack-of-All-Trades, you'll be a Master-of-None. Gil vs. Time differs between individuals; if you have the time you can turn sand to gil. MB is for the ones with limited play-time.

Whole Sale:
As a Gatherer: I put a stack of 99 of Item-X for 100 gil (9.9K Gil total), also I put a stack of 20 of the same item for 150 gil (3K Gil), usually the latter sells since the buyer doesn't need 30 pieces, or even buy 1 piece for 500 Gil. This is the concept of whole-sale (Stacks) and Retail Sale