From my experience, I did gain more Soulstones in the higher training missions that costed me more than 30tp each step, so overall the results are pretty much the same.
Vials and other BT/stat boosting arena items will give the same results as well.
I think the only time a certain training mission can work to your favour would be when you're farming for feeders or searching for monsters during training events (1-1 being the most popular choice).