To begin, since you obviously have some kind of problem, I'd turn off the auto watering and water according to good practice, which is when the soil about two or three finger joints deep is no longer moist. Properly done, you won't be watering more than about twice a week.
Now, you observed the roots and probably correctly deduced that they were not being drowned, even though water is getting in. Therefore, consider that they are going short of water. The draining nature of soil has a lot to do with it, but tomatoes want about 2 inches of water a week. So for a container of 12 inches diameter, two inches is 226 cubic inches of very close to one gallon per week. If you have a lot of pebbles or perlite in the mix, it might take more.
I'd discount the bumps. Tomoto hide gets rough.
The splitting supports the idea of being habitually short of water and getting periodic but inadequate waterings. Perhaps brief daily waterings that do not maintain soil moisture.
