I've noticed that the 40 slot pickup tower container in modded games with lots of drops and their various qualities, is a real bottleneck. My best guess is, that you intend to keep it limited to 40 slots for UPS reasons since afaik scanning large slot inventories causes lag? How about modifying the container stack size then? Main motivation is to keep the amount of pickup towers as low as possible. Also I know you can get more slots via quality, but that also raises radar coverage, which might be an undesirable side-effect.

Comparison between steel chest and pickup tower. Both inventories have the same type and amount of items, but different stack properties:

PTpt.lua line 182 additions:

    inventory_size = 40,
    inventory_type = "with_custom_stack_size",
    inventory_properties =
    {
      stack_size_multiplier = 10000,
    },