Change the setting Add Store Code to Urls from global setting to Store Name setting
Currrently the setting Add Store Code to Urls is a global setting. This should be changed to one level down: Store Name level.
One should be able to run 2 brands like this
Brand AAdd Store Code to Urls = YES
nl site = brandA.com/nl
en site = brandA.com/en
Brand BAdd Store Code to Urls = NO
And different Base URL's
nl site = brandB.nl
en site = brandB.co.uk
Curerntly when Add Store Code to Urls = YES the /en, /de, /fr, /nl are added to all stores in a multistore setting. In this example brand A follows this model, but Brand B does not and has unique domains
Please change Add Store Code to Urls to Store Name level (instead of global setting).