It depends on how your branchmap is configured.
If it is just a basic stream set up then yes robomerge should respect it in so much as robomerge is just issuing perforce integrate commands using -S which use the stream view for determining which files to merge and perforce should not be merging the isolated files.
If you’ve configured a branchspec for the relationship between the two streams then you will need to add a filter in to the branchspec for that folder as well because isolates in the stream view are unknown by the branch mapping and it will continue to pull the files in.