Getting most items in the mod can be automated using only vanilla + mod items, or can at least be done in bulk. The exception to this is the runic alter, which can be extremely grindy. So my request is for an in-mod way to make the creation of runes (and preferably all altar use) more player/automation friendly.

Since we can use a dispenser for the wand, drop items, and get a signal out of the altar when ready, the only thing really needed is a way to put/pull sets of items into the open crate or altar.

Some ideas that try to stick with the theme and avoid GUIs:
A general use transfer flower- upgraded hopperhock or spectranthemum, or a hopperhock + spectranthemum hybrid. It will pull either one item, or a set of items from the inventory it is facing and place them in the inventory behind it (or that it is bound to?). A chest on the sides or top can be used as a filter for a set. The transfer would occur when the flower is given a redstone signal or mana burst, and if a filter is present, only when a full set is available.
** The problem with the spectranthemum for this is that the items have to be on the ground (so even if a filter possibility were added, despawn is an issue).

Another type of crate or upgraded open crate. It will only accept items that match it's filter chest if one is present, and only the same number of each particular item. When pulsed it will drop everything at once and prevent pickup for 10 like the crate. It a filter is present, it will not drop if a full set isn't loaded in.

An add-on for the runic altar, say a runic pedestal or something. When pedestal or alter are given a pulse (and/or maybe when the altar creates an item and clears, for chaining) the altar will pull items from any adjacent chests that are needed to craft the item on the pedestal and start crafting it. There could also possibly be an upgraded version of this that holds a few items and the altar will do a round robin approach with them. The altar would only every pull the items if all items needed are present, so no partial pulls that could mess up automation. With a pedestal, comparator, and chest, plus an open top for the final living rock to arrive, that would leave one side and bottom free for incoming mana.

Sorry, I'm kind of behind on versions. Came back to close this after I saw all the new corporea stuff, but you already did.