This is the part where not having persistent directories bites B2. On a normal backend, rclone would have created the directories already and these would be on the remote. But they aren't found here.
So I think you've confirmed it is the B2 directories issue.
I've had a go at fixing this.
When adding a Virtual on a backend which can't have empty directories, if the directory isn't found then rclone will create it and all of its parents.
There is quite a lot of new code here so it might not work properly and it needs tests for the new code, but I thought I'd let you have a go first to see if it works.
This should emit a new DEBUG Creating parent of virtual directory since backend can't have empty directories
Please give this a go
v1.61.0-beta.6591.3f77e5648.fix-vfs-empty-dirs on branch fix-vfs-empty-dirs (uploaded in 15-30 mins)