When I want 1400 WT I need 1k and FOUR x 100k tokens, NOT 1000 and 250 AND whatever is left. Please, please do something!
Unfortunately, something like that simply cannot predict what denominations someone would prefer their items to be in. It's always going to go in order of highest denomination, and then next highest, etc.
If there's a specific denomination you prefer it be pulled out in, like your example above, you can simply remove 1000, then 100 four times, and you'll get what you're looking for!

I always wanted there to be a more specific withdrawl system -- "Give me 1, 1k pt token", etc -- but it probably won't happen and I can see the logic being kind of a pain.
I wonder if the site could implement something like the battle token trading page for wizard tokens? The different tokens would be listed by denomination and you choose which ones you want up to the amount of your withdrawal.