I've confronted this too. Here's how I dealt with it. I have an upcoming trip MIA - JFK - YYC, ticketed on Delta but with the JFK - YYC leg on Westjet. Selected MIA - JFK seat no prob online with Delta but unable to select Westjet seat JFK -YYC. I have a 1st world horror of being assigned a middle seat on any flight, but particularly one of 5 hours +. So I messaged Delta who replied pretty much instantly with my Westjet confirmation number (well done!), so I duly logged on to Westjet.com to select my seat, only to be advised this was not possible (why?) and I needed to call them. I duly did and the phone was answered very quickly by a helpful agent who assigned an exit row seat for me (praise the lord!). While paying the seat selection fee, there seemed to be an issue with my address (I live in the UK) but this was quickly resolved and my seat selection for the Westjet flight now shows on my Delta booking. So not seamless, but very do-able.