I figured out the problem! The mod disables roboports by setting construction_radius = 0, which works for most things, but an occupied vehicle's distance from the driver is 0, so the bots are allowed to work on it. Setting robot_limit = 0 fixes it--now disabled ports simply aren't allowed to launch robots at all. Just add this line to the mod's data-final-fixes.lua file, before "data:extend(equipment)":
processEquipment("roboport-equipment", {["robot_limit"] = 0})