First off you need to get the roots set in a solo cup before final transfer......Roots should be nicely seen at the edges, when you slide the cup off....They should be not to the point of making circles around the bottom of the cup.
Next off, you will kill any advantage you would get from a SS by re mixing as you say.....so NO......do the layering !!!
Put some SS around the edge of the pot, does not have to be a thick or large amount, just there where the roots will circle the pot. It makes more SS nutrition available to the plant. Easy to do it when layering as vs attempting to make a "layer" around the edge first.
I don't like smart pots....They dry out to fast and tend to get the umbrella effect easy.......Look up Plant Warrior pots,,,aw here,,,
https://www.sunlightsupply.com/shop/bycategory/pots-containers/plant-warrior-pots
How big do these auto's get? If bigger then 24",,, you might consider the 3 gallon one's...
Remember, Roots first,,,then trans to layered pots......