The hidden inserters are set to only pick up one item at a time no matter what, so I can keep track of what goes where and they don't end up holding any excess.
I looked into your comment about it feeling less responsive, and I couldn't help but agree. In the new release (0.16.31) I reworked some systems to improve responsiveness at the cost of performance. If too many people have trouble with the performance, I may have to revert these changes.
Notice that any entities not on "nauvis" (those inside factories) and any entity that can move (trains, cars) don't use inserters and are instead supplied by the script. If these entities aren't being supplied quickly enough, try increasing the "inventories per cycle" option to supply them more quickly.