If you plan on using your USB 3 ports to transfer USB to the VM then you need to configure the controller as USB 3 - The system cannot communicate with a USB 3 controller unless it is defined as such.
Filters tend to confuse and you don't need filters - just use the mentioned methods to attach the USB stick when required and use eject from the guest system.
If you insert an USB and you have a filter defined - it will be immediately attached to the VM - and in case you didn't want that - you have the confusion.
The settings can always be changed when the VM is shutdown. You can do it exactly as you want to so feel free to do it your way. Experiment with it and find the way that works for you.
And most importantly - have fun... And when something acts weird jump back to the tutorial
The tutorial is by no means meant as it is the only way. It is a translation of a Danish tutorial I made for the local community - one guy specifically which has been confused by the VirtualBox website.
He attached his mouse to the VM and every thing went haywire. He also added filters and could not understand why the usb was not visible in his Linux system. In fact he fumbled so much with it I had to bend it in neon before he understood what was going on
He even tried to install drivers for the basic USB in his Windows VM. He was very persistent and kept explaining me it was absolutely necessary - until I convinced him to insert the VirtualBox Guest Utils and install them. Then it worked.