This is not just valid for France; this is the standard 'tax residency' rule for all EU countries.

However, in reality; I have never heard of any cruising liveaboard with an EU flag that had ever had any problem with this rule in another EU country. The tax authorities are not interested in yotties, they are more focused on residents with properties. Now, if you are in a Spanish marina and you have clearly been there for years and never moved; you might have a problem. Otherwise: relax. That is not a guarantee that you will never be checked, but I think the odds are better that you will win the lottery before this happens. (and then they will be interested.....)