I don’t fault you for having the second box on there - it may not be completely necessary in central CA but certainly not wrong.
The logic you used - that they were out of space in the first box so you added a second - applies to adding the super too. But it’s no problem to remove an under/un-utilized box. The bees will thank you for it.
The queen, nuc, and package sellers have to have strong enough colonies to split so they probably have greatest availability in mid to late season. They can’t get queens mated too early if there aren’t enough flying drones too. So, April 10 really doesn’t seem late to me. In Ohio you’re lucky to get a good strong nuc in late May.
The reality is that a first year colony probably just has to be nurtured and you shouldn’t expect a honey crop from them anyway.
But you’ll be ready for next spring if you feed them well (white sugar and water are cheap), treat them appropriately for pests and disease, and protect them from robbers and predators!