I like the new layout much better, and I'm amazed by how good that anubias looks now, hooray for amanos!
You should be fine with inert substrate, it's what i have in 2 of my 3 tanks without problems, I add root tab to the substrate and the plants are fine, crypts grow really well for me even in my inert substrate, in fact currently they're doing better in my 10g (inert) than in my 30g that has "plant substrate"
So don't worry about that aspect. Any aquarium root tabs you can find should do fine, I used to use whichever ones were in stock at my local fish store, I think you can find larger quantities at a better price online though (i forget the brand though, so you can wait for someone else to chime in on that
) In fact, one of the vendors on here might sell them.
As for cutting the crypt roots, I've never done that, so I can't answer for sure, but the large batch of roots getting in the way of planting the crypt very deep in the substrate is actually good because the rhizome
(the stem-like part that runs along the substrate that the leaves grow out of) needs to be kept above the gravel because it requires light to keep the plant alive. As the crypt acclimates and begins growing, it should pull itself a bit closer to the gravel as it extends its roots
Also, don't get disheartened if the leaves start melting, it's very normal for crypts to do that when put in a new tank, or moved around, or even if you look at them sideways
but it should bounce back and start sending out new leaves, so don't give up on it!
Sorry for the novel, but I figured I'd chime in with any potentially useful info I could think of