I don’t know what changed.
Using a Cartfile is definitely another valid option. I haven't ever actually had to setup Carthage with dependencies like that so I won't be much help. Your "challenge" there will be keeping the SwiftPM and Carthage files for sure using the same builds of the dependencies. That isn't very difficult though.
Yes it is sad needing to support multiple tools for the same task. I know that many of the goals that have been stated for SwiftPM will hopefully remove that need at some point.