Since no train conveying fare-paying passengers has ever worked over the connection between the main line and the branch, because it isn't passed for this at all in its current condition, no, the restriction applies to the use of any part of the branch by passenger trains.
There was the inaugural train run for the volunteers and corporate sponsors who made the revived Branch possible, which did run onto the branch with passengers onboard, but no fares were charged. That was when it was discovered that the curves were really too sharp for the liking of 63ft coaches.
When the branch does run passenger services (12 days a year, if I remember correctly, is the maximum permitted) the train runs ECS over the connection and then shuttles up and down on the branch.
Come and have a look this weekend 25 & 26 March - the first two Branch Running Days of the year!