Resellers can elect to sell a product at any price they like. Always have been able to.
The loss is theirs to absorb.
It's very possible that some companies over estimated the demand, and have excess quantities to liquidate.
It's also possible that some companies are willing to absorb the loss with the hope that a customer will spend additional money with them.
Apple can only enforce pricing at stores they own. Otherwise the price is generally determined by a combination of what the resellers pay to get the phone, and what customers are willing to pay.
Resellers always take a gamble on items they purchase to resell. The need enough to handle demand, and hopefully don't pay more than... or purchase more than consumers will buy or pay.
Personally, in the current product line, the SE is going to be a hard sell. Unless it is priced cheaply. I would be a buyer if I needed a new phone... but I love my iPhone 5. Great phone, reliable, does what I need, and it's the right size. If I needed a new phone, I'd be after the SE. But... I wouldn't pay anything close to what an iPhone 6 or 7 series phone costs. So that's its pricing dilemma.
As for why Apple still charges more for the phone than the current resellers are liquidating them for... its Apple. They traditionally don't decrease prices of a current model phone or computer unless a new product shifts it down the line.
Apple is also confident that they aren't overstocking themselves. And any SE's that remain after it's discontinued, will be sold in the refurb store on their sales page, or held for warranty replacements.
So it works for Apple to still have leftovers if it happens. Resellers want to get whatever they can, while they can. They don't want to get stuck holding an overstock of any item that has zero demand left. So if they have to take a loss to sell it out while it still holds interest, they will.
