The main page says "prior to version 1.1.0, filtered pipes had to be placed right next to inventories".
If I have a non-filter pipe between a filter and a chest, the filter is ignored.

I assume the advanced filtering option "Persist to Other Pipes" is what determines if the old behavior (filters not next to inventories are ignored) applies or not. I tried it with this option both on and off, and saw no difference.

Yes, persist to other pipes is the correct flag for the situation you described. It should be fixed as of v1.2.1. If it isn't (🤞) just reopen this again.