Answering my own question here, but hopefully someone will find it useful. We stopped using the Shopify GA code insert field and opted to copy the new remarketing code (pasted below) into the <head></head> of our Shopify template. Everything seems to be working properly so far...
Talked a bit too early. E-commerce tracking went awry after I put the code to the header. So I reinserted the UA code into admin and left the header as it is. E-commerce tracking is back to normal but I'm not sure about the remarketing list. I guess I'll find out when remarketing stops to the existing list.