Would it make sense to add an option to decide if the global filter has to be applied to the vector layer and/or the join layer only?
In a number of situation, the vector layer may be a background map (eg. admin boundaries) that user will join with other sources to render thematic maps. But when you enable "apply global filter to layer" then the filter is applied to both the background layer and the joined one.
When building dashboard embedding the map, then control and other viz will focus on the joined layer usually and the global filter should not be applied to main vector layer (which will return no features, and map will be empty)
What do you think ?