I usually sleeve the cards on card heavy games, so regular shuffling doesn’t work for me. Usually, I will give some cards to another player or two and we will all do some shuffling of those cards, then hand some of the cards from our pile to someone else, while taking some of their cards and shuffling them into the group I kept.

Doing this allows for the shuffling to be divided by a few people, making the amount of cards being shuffled by each individual more manageable. It also helps to get the other players involved in set up, which can keep them from being bored.

With nice stiff sleeves, I cut the deck into manageable sizes, then push the bottom corner of one stack into the middle of another stack until they’re riffled with each other.

I do that until every stack is paired with another, then cut the stacks and mash them into an unpaired stack.

Keep doing this until all the stacks have cards from every other original stack in them, then get somebody else to stack the stacks in whatever order they want.

Sometimes I also just leave the deck in multiple stacks (as you mentioned, Ark Nova’s deck is huge, TM as well, and with sleeves can be impossible to stack high) and let people take the top card from either stack. Obviously if the top card of the deck can be manipulated then you need a rule for what happens in that case.

For Ark Nova before we place the board we do something like this

A deck for the Commander (EDH) version of Magic is 99 cards; usually sleeved. With good-quality card sleeves, “mash shuffling” usually works pretty well: split the deck in halves and just kinda push them together edge-to-edge, using the shape of the sleeves to help.