The best way to make money off running a market will probably be the percentage based approach. When I first thought about it, I thought price per volume would be a good way to go but now that I've thought it out a bit, I don't think that would work very well. For instance, I initially thought that since almost all goods will take up physical space in the market area, the main limiting factor for a market (at least in the beginning) will be pure volume of storage space. So for bulk items like basic raw materials, it would probably make sense to charge per cubic units of storage space. However this does lead to several changes in market behavior:
Not every item will have the same ratio of price to volume, so the percentage cost for lower ratio items would be much higher than for higher ratio items. For example: Say you charge $5 (is there a term for the in game currency yet? idk) per cubic unit of space. Item A sells for $20 per cubic unit and item B sells for $100 per cubic unit. That would mean 25% of item A's income would go towards the cost of selling while only 5% of item B's income would go towards the selling cost. Therefore, as it's 5 times less profitable to sell item A as it is to sell item B, merchants will likely start to favor items with higher value to volume ratios. These higher value items may have a lower velocity (the rate at which they pass through the market), so you may end up with a lot of stagnant orders waiting to be sold.
TL;DR: I guess long story short is go for a percentage based approach. It's just less headache for everyone and shouldn't affect market behavior too drastically in any particular direction.