After testing this some more I have found out, that the cause of this is not the vehicle itself, but the change of the fuel value:
data.raw.item["rocket-fuel"].fuel_value = "20MJ"
It turns out, that the burner has (an invisible?) maximum capacity depending on the fuel type. That means despite inserting the fuel amount manually, the maximum for entity.burner.remaining_burning_fuel will always depend on the fuel type.
That means this what I do...
entity.burner.currently_burning = "rocket-fuel"
entity.burner.remaining_burning_fuel = 100000000
... will throw no error but it will result in the vehicle having only 20.000.000 J instead of the 100.000.000 J energy.
I'm not sure if this is a base game bug or intended behaviour, but I guess I will have to create my own fuel type, to be independant from other mods.
TLDR: You are doing everything correct ;)