Clinical Studio was created to be an internal solution for its users. As such, it can be customized from the top down for your own studies. The site appearance (theme) can be customized for the account as whole and it can be customized per study. This is why a similar Theme Manager option is seen in the following two locations:
To elaborate, If there are multiple studies running on your account, the appearance can be set to dynamically change when you switch between those studies. If the theme is not customized at the study level, it will default to the account theme. If the account theme has not been customized, it will default to the native Clinical Studio theme. Here's an example of a site that has been customized:
Continue reading on how to customize your theme.