Thanks for the suggestion.
We like the idea of adding padding option, so here is a new beta:
This beta works with the following diagram:
skinparam ParticipantPadding 10
skinparam BoxPadding 20
Alice -> Bob : hello
This kind of modification is quite easy to do (when you are used to PlantUML code...), so we did it directly.
The setting can be set in pixel only (which is consistent other values).
Other padding settings may be implemented on demand, so please ask!