This is a know issue that we have discovered and creating this issue to document this as a known bug. See the original bug report in matomo-org/tag-manager#158

Bug report:

• Configure a JS tracker which calls setCookieDomain with value .example.com
• Load the website www.example.com
• Got: Two cookies are created on domains .example.com and www.example.com eg.

9b1feac345884afb.1553796770.0.1553796834.. on domaine www.example.com
97b1f55eea218e3e.1553796770.1.1553796834.1553796770. on .example.com

• Expected only one cookie on .example.com

More details:

• we we call tracker = Piwik.addTracker(trackerUrl, matomoConfig.idSite);
• which then triggers the line setVisitorIdCookie(); in the Tracker constructor
• which creates the wrong cookie on www.example.com
• the wrong cookie is created because at this point, the function setCookieDomains hasn't been called yet. It's called a bit later in: https://github.com/matomo-org/tag-manager/blob/0.2.6/Template/Tag/MatomoTag.web.js#L121-L123