There's nothing there that support couldn't fix but beyond that Steam and Larian want the game to sell so I can guarantee you there won't be any issues around "Oh you bought SEA so we won't let buy the CE because it's a different download."
I get the feeling you have never dealt with Steam's support.
For the record, I can't buy the Digital Collector Edition on Steam because (as far as Steam is concerned) I already own that content because of my Early Access purchase. It will not allow me to add the item to my cart and purchase it for myself (not that I want to, but I tried it as a test). The same holds true for the standalone Source Hunter DLC package, I'm not allowed to purchase it and add it to my account.
I've also had Steam take upwards of 3+ weeks to get back to me on a simple ticket submission with a simple request. And that is, unfortunately, pretty normal for Valve. Right now I have a ticket going with them for the DLC package problem, sitting there after 5 days untouched. I'm not expecting a resolution anytime soon.
