It's a side effect of using stacking slots and a shared inventory on a surface. Inventory filters are only supported on non-stacking inventory slots, so it's a trade off on which is used by the mod.
The shared inventory per surface is a requirement for keeping the code simple and performance high.
So the design options are:
1. shared inventory + slot filters
2. shared inventory + stacking slots
Going with option 1 means the chest needs a lot of inventory slots to handle a high consumption scenario (like Rampant++). It's possible to add hundreds of inventory slots, but that impacts UPS; it's expensive to scan every slot in the chest for contents.
Going with option 2 means that the chest can store a ton of supplies in a few slots, which improves UPS, and works for high consumption scenarios. But the trade off is that you can put other things in there.
If the factorio API changes in the future to support both options concurrently then I'd be happy to add it.