I think you're right about the so-net recharge option. I bought the So-net one for a family member two years ago, so my memory is kinda fuzzy. It's best to just buy one card first instead of three together at the same time.
I had two bad experiences with IIJmio before, so personally I would not recommend it to others. One of them is when I bought IIJmio tourist prepaid card and the card stopped working on second day. When I called them, they said they cannot replace it. If I want a new sim card, my only option was to "upgrade" the sim card to a monthly plan. There's no way I want to sign up for annual plan just to replace a broken 3000 yen sim card.