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As you can see in these screenshots, when I hover over the furnace, only a single inserter is highlighted, while if i hover over the missing inserter, it shows the right pickup and drop targets

Thanks for the report. The inserter interaction logic currently does not care about custom inserter pickup/dropoff abilities and I don't consider it worth the performance implications of adding support for them. If anything I would change it so if an inserter is using custom logic it doesn't show the highlight at all unless you're hovering over the inserter itself.

I think it's good enough as it is, i just reported to let it be known, its just that in this case (a very corner case inside the modded corner cases) it's barely touching. Dunno about removing it, it's useful for me in 99.9% of the times where it works as expected