These are public houses owned (usually) by a brewery. The manager, an employee of the brewery, runs the operation. The retail sales of beers, wines, spirits, etc will be supplied by the brewery, who will be required to account for VAT on such sales.
The brewery may franchise the catering side of the operation to the manager. In this instance, the catering services provided become a private enterprise of the manager and, as such, these activities are considered separately for VAT registration purposes. The normal registration and liability rules will apply if the registration limits are exceeded.
A public house does not have to be owned by a brewery to be a managed house. The term can apply equally to circumstances where the owner of the premises is not a brewery but runs the business through a manager. The owner is then the person liable to be registered for VAT and to account for output tax on sales (subject to the comments above regarding catering).