Just to follow up on this for anyone else curious about Costco packages for S&D with tickets...I called Costco Travel and spoke to an amazing rep (Jeremiah) who knew the answer to every question I had.
Confirming what I thought, when you book a refundable package with tickets through Costco, you do NOT get the ticket portion refunded if you have to cancel. It is treated like a credit with Disney and you need to work with Disney directly to rebook tickets for a later date, pay the difference, etc. The price you pay up front for a refundable rate is basically the ticket cost and a small hotel deposit (that part is refundable).
Also, as far as changing your tickets after booking, yes like you said it would have to be done through Costco and not Disney since they are essentially the ones buying your tickets for you. The rep said they basically cancel your tickets (and like you said, you lose your park reservations) and then purchase the new tickets for you and charge you the difference.
I was curious about that because we were not planning on paying for anything until August, so I'm looking to spend as little as possible right now since it wasn't in our budget for this part of the year haha. If I can save the difference between 5-day hoppers and 3-day base ($605) and just change my tickets later, that helps a lot. And it appears that I can.