Hi Alin
This could work by having two 'placeholder' courses with no activities in them that are part of the Certification.
The course completion condition would be manual completion by others and select the trainer role
The certification would have the first course as the second to last course set with the 'Then' condition for the second course in the last course set.
This would require the first course to be completed before the second course is able to be enrolled in and completed and messages such as course set completed could be setup so the learner knows what step to take next.
Does this sound workable?
Regards