It wouldn't be more convoluted. Right now there's nothing more annoying than having to break down the 200 items I have into stacks of 10 and list each stack one by one because I know the stacks of 10 will sell while no one needs a stack of 99.
So I list two stacks of 99 and players buy however much they want. Eventually the stack size is reduced to zero or small enough that I cancel the listing to relist a higher quantity if I've got more of the same item to sell.
In the meantime instead of my retainer having 20 listings of the same item, my retainer has 2 listings of that item along with 18 other items for sale. I've got more selection on the market overall and that means more appeal to more buyers instead of relying on a specific type of buyer for my profit. If something doesn't sell, then I know I need to reconsider what I'm listing or the prices I'm listing at.
As for the earlier comment about everyone listing the premium price per item if partial stacks could be bought so buyers end up paying more, it will never happen. If everyone is listing at the same price, you have no guarantee your stack will be the one the buyer is choosing. People will turn around and start undercutting each other to get their stack moved to the top of the list so it's picked first. That will drive prices down until they reach existing market rates because those are the prices people are comfortable with for that item.
Flippers will still be able to make gil by picking up the stacks listed low to get dumped faster though if the system did put them out of business, the majority of the player base wouldn't mourn it. A lot of flippers aren't even making their money off reselling stacks. They're making their money off the items that don't stack and such a change wouldn't affect those items.
I've played games where players could buy partial stacks and my profits were doing just fine because my inventory turnover was faster. Few players are going to buy huge stacks when they only need a small quantity but they won't hesitate to buy when they can get just the amount they're looking for. It also gave me a much clearer picture of where the real demand was so I could focus on those areas instead of trying to guess what players really wanted to buy.