Noted! I did trip on this myself a few times, but it was always my conclusion that the shorter second command was an indication the initial one was too long for nothing. Your example is clear, though. The upcoming version will support adding explicit files one by one, and forcing them a specific command. But for matched files from a monitored path, the last command used always overwrites the previous one.
Since I still believe the current behavior is valid, I'll target adding a "Keep initial command" option somewhere. You'll have to turn it on, it will be off by default.