Not sure about the seat upgrade — I’d imagine upsell offers are not refundable; if you want to upgrade your seat, you should hit “modify flight” to directly reticket into a higher cabin with a refundable fare. There isn’t a fee for doing that though I imagine it will be more expensive than an up sell.

As for the refund, if it was marketed as refundable I don’t see why there would be a fee. I’ve had no problem getting 100% back from refundable fares in the past.