Still getting some issues when trying to set process custom properties and get it using worklflow service API.
Following axel recommendations, I did the following:
1) create aspect with optionnal properties and add it as mandatory aspect to process start task model
2) set these properties in ScriptTask / Scriptexecution listeners.
I defined two process listeners (org.alfresco.repo.workflow.activiti.listener.ScriptExecutionListener): one on 'start' event, one on 'end' event.
When setting the custom property by script on start event execution listener, property is set and accessible using workflow service. When setting the property on 'end' event (or from any other ScriptExecutionListener/ScriptTaskListener), the property is not set (or not visilble from workflow service).
Just to complete this topic: as Axel explained above, any process property can be set from task/process activiti listener and read by workflow service as soon as the property is defined as a process (start task) property.