I can't find more precise informations, but the European quotas for Japanese cars were said to disappear at least one year before the start of the French production of the Yaris.

As you say in the first linked page, Sandie, French production started in 2001 only. The TMMC corporate site says more precisely January 2001 (fr - See the bottom of the page), which means indeed that none of these 124 1999-2000 models should have the Made in France flag.