Didn't read everything, but I really like the idea of a listing fee to prevent people from changing prices every 5 minutes.
Just remove tax from a sold item and use that as listing fee. And get rid of the different taxes/fees per nation.
If the item doesn't sell after a certain time, return the item and the listing fee.

Or limit item listing to, for example, 6 hours. So you put up an item for sale and can't take it out or change price for 6 hours.

I also don't see where the problem with fees would be. You need a few thousand gil to be able to either put something expensive or many cheaper things for auction.
If people don't have that kind of money, how can they repair their gear, or buy materials?
I don't see a problem there.
You wouldn't lose money. If you sell something now, you have to pay a tax. Paying before or after someone purchases your item makes little difference if you don't sell 40 items for 100k each.
And if you do, I'm sure you have the money to back it up.