Initially this was my first idea and preference. So I increased the start-delay of the Raspberry without any improvement. After investigating it appears that the delay is the time between the on-signal and the first command like setting the input. The configuration-tool did not help either. Between the on-commands of the devices no delay possible. Only before additional commands.
It is hard to find in the harmony software respectively on myharmony.com or whatever you use for programming. I've captured how to find the setting:
I own an old Harmony 900 remote, so I have to use the old software. I assume you are using the myharmony.com website for programming, but the menus are quite similar. Perhaps you can find this setting there as well