Yes, that is intended.
Elite Dangerous, Planet Coaster and Jurassic World Evolution each have their own forum theme, which cannot be changed by setting a user preference for another theme (due to a limitation with XenForo). If a user changes their preference for a forum theme, then that forum theme will be applied to all "neutral" forums, in this case the Homepage, Frontier Developments, Frontier International and Off-Topic.
There is currently no way to change this. The team is aware of the request of many forum members to enable changing the forum theme on game-specific forums, and will get back on this matter in case anything changes regarding this matter.