Bony structure under medial malleolus bilaterally, no pain w/ compression, tibial nerve is palpable, mild flat foot. Could it be misaligned calcaneus?

Misaligned talus. Is usually what happens with what you are describing. This happens in a pronatory foot. Orthotics are good conservative treatment. An implant between the talus and calcaneus is a surgical option.
Hyperpronated. You're describing foot structure consistent with being hyperpronated.This is associated with flat feet. You don't have to be that flat-footed to be pronated. Your bone structure under your medial malleolus will be prominent. I doubt you're feeling your tibial nerve, it's probably your post. Tibial artery. Being hyper pronated could lead to a lot of problems. Address this. Are you symptomatic?
Tarsal coalition. A bony protrusion under the medial malleolus maybe be a sign that you have a tarsal coalition of the ankle bone (talus) to the heel bone (calcaneus) especially if the flatfoot (pes plunus ) is associated with stiffness of inversion and eversionof the hind foot. A plain xray and or a MRI or ct scan of the foot will confirm what the situations.