My experience is supported by the Article 6 wording and means your son will be ok.

My experience: back in the days before I had an EU passport I travelled on my Australian passport. I spent 90 days under the Schengen visa waiver program. During that time I applied for a Swedish partner visa which gave me 6 months. I contacted my case officer and she said I could go "back to back" with another Schengen waiver period immediately following the partner visa 6 months. To be safe I chose to leave Schengen on the last day of my partner visa and re-enter on the first day of my second Schengen visa waiver period. I had no problems at all.

So my timelines was 90 days visa waiver, 6 months partner visa, 90 days visa waiver. About 12 months in all.

If your son has a case officer he should contact them for confirmation.