Simply put, it is a bit of a pain to deal with if I want to block out undesirable hulls like most of pirate pack. You may think all you need to do is click all of what you want and it uses just that right? Maybe.
For ships, it seems like I need to click at least one hull of each size. Afterwards, I need to go through each sub-category of Warship, Carrier, Phase, and Civilian and make ship at least one ship type is checked to block out unwanted hulls. On top of that, civilian may be sub-divided by tankers and cargo haulers. I need to make sure I have a tanker and hauler checked, if I do not want the very slow Atlas and Prometheus slowing down my patrols. Then, there are some ships that may fit into more than one category, and they are not always immediately obvious. For example, Gemini. It is a hauler AND a carrier, but the screen only makes it clear that Gemini is a carrier. It is nice that I can replace civilian haulers with Gemini, but on the other hand, I do not want too many Gemini if I want mostly carriers; I want the other dedicated combat carriers like Drover or Heron instead.
I have no idea how weapon priority works for ships. Do they replace weapons on default loadouts? If I want custom loadouts with weapons I like on my ships, is that all handled by autofit. Do I need to delete default autofits and replace with custom autofits if I want to produce ships with those weapons pre-installed? Currently, I use weapon priority primarily to arm battlestations (so they use Tachyon Lances instead of Autopulse Lasers), but I would like to change the default weapons my ships get after Heavy Industry produces them. Is that handled by priority or custom loadouts from Autofit?
Fighters seem a bit easier to observe. Like hulls, I guess they are divided between bombers and non-bombers, and work from there.