Items hidden at runtime are not filtered out of displayed recipes

[Seraphaestus]

When I have items hidden through REI's in-game manual filter, recipes involving that item are also hidden. However, I am using KubeJS scripting to remove items at runtime (so they can be dynamically added as part of custom item staging), and this does not cause the associated recipes to be hidden. This is using the removeIngredientsAtRuntime function of the ingredient manager. Not sure if this is a feature that comes from REI's JEI compatability stuff.
I feel like I had this working before, but I'm not sure what's changed (I may be misremembering it just working with the manual filtering). I've tried going back a version on the relevant mods, and looking through the settings, to no avail. The Should Filter Displays setting is on.
This is on Forge 8.3.571.
I'm making this as a discussion instead of an issue because I don't know if the issue is in a lack of understanding of how filters work, maybe a setting I've missed, on the KubeJS end, etc.