Hey.
I solved this issue by manually setting the extensionIDs in the .env file. The cli will read from this to automatically match extensions.
You can get the Ids for the existing extensions by looking at your version 0 (the first deployment after switching to simplified deployments) and manually going into each extensions and looking at the network request. Inside the request payload or response (can’t remember) it will contain the Id. Copy this into your .env and then manually deploy from the cli to your production environment once and afterwards it should automatically match without issue.