I'm on NeoForge 1.21.1 on the latest version of the mod and the filters don't appear to work.
I don't want the hopper to let vanilla wheat seed through, so I put those seeds into the filter gui and set it to exclude mode. Then I put it in the proper filter slot inside a gold filtered hopper and it just lets the seeds through anyway. This happens when a vanilla hopper is feeding into the filtered one. I notice that when the seeds are not supposed to be allowed through and they do anyway, they go through at a slower pace to all other items.

As a temporary measure, you can point the vanilla hopper to the side instead of directly into the golden hopper. That way only the desired items will get pulled through.

Wanted to share my workaround! Using a double chest, you have four ways for Filtered Hoppers to pull items out of the junction. This can be multiplied by using a non filtered hopper into another second chest for seven total ways, or so on.