I think you are going to have to decide whether you want to grow this tree as an outdoor specimen tree or a bonsai (they do make great bonsai as well). If you want a healthy, adult-size ginkgo eventually, you need to put it in a bigger container at this point. I would say a minimum of a one gallon
container. Your little tree should also be in full sun. I have all kinds of wild life in my yard as well, and occasionally something gets nibbled at but that's the chance you risk in the great outdoors I guess. How cold does that porch of yours get over the course of the winter. If it goes
below freezing on a regular basis, it is too cold. Roots growing in a container are exposed to much colder conditions
in the winter than roots growing in the ground. I overwintered a containerized ginkgo for several years in an attached garage that never went below freezing but was cold even to bring dormancy (between 40-55 F. for coldest part of winter). I hardly watered my plant over the course of the winter under these conditions (maybe once a month) during mild spells. Also, you might start apply a very mild fertilizer while it is in active growth. Hope this was helpful. Good luck!

Alright, I'll move it up to a bigger container. I was hesitant to do this 'cause I was worried that there'd be too much soil and it'd stay wet too long and cause rote, but if you say go for it, you've got more experience here than I do. Should I go for more surface area, more depth, or about even? Surface area would give me faster evaporation, I'm assuming, but I don't know whether ginkgoes have shallow or deep root systems.

Garage doesn't get below freezing in the winter (or shouldn't, at least) but definitely gets cold.

One gallon is really not considered too large for a seedling.
Normally, I underpot (grow plants in pots most people might consider too small). But with a tree, you need to give it space. I'm not sure why you are worried about excessive wetness. If the soil is well draining and it is reasonably warm, a plastic one gallon pot outside in full summer heat dries in NO time. I tend to use a lot of plastic pots that are about 8 inches deep and five inches wide (guestimate). Currently have a lot of seedling palms and bald cypress in this pot size. Not sure about their root structure, but they really are adaptable and pot size dimensions are not likely to damage them. Rotting is more commonly a problem with tropical or xerophytic (arid-loving) plants in chilly to cold temps. Good luck!

Repotted this recently. I wasn't going to move this up to a one gallon pot right away. Then I removed it from the container it was in and the roots all sort of untangled.

Definitely rootbound, but more than that, the tiny container it was in was creating this very weird optical illusion where the tree itself looked a lot smaller than it really was. Does that make any sense?

Anyway, also moved it to a sunnier location. No new leaves or height, but the trunk's noticably thicker, and I can see little green buds further down on it. Should the apical bud be doing anything interesting?