that's strange, as I think all ship commanders improve their main ability when practicing. That's sure for surveying vessels, jump gate construction ships at least, I was expecting it to be working with terraforming and mining.
They don't improve the same way as teams (geosurvey, Xeno ect). If you see improvements it will likely be to do with their promotion score and the fact they are "active" as opposed to being unassigned. This has been as far as i know. Someone might have more detailed information regarding this.
I don't seem to see any of the Asteroid miner and Terraformer ships to train their corresponding abilities. It's probably been up to 5 years that i have some in my fleet now.