There have been instances in MtG tournaments where players have been banned for manipulating their decks, even after a ripple shuffle. They would take their cards out which were stacked a certain way, so for example all lands on the top, then ripple shuffle so they were nicely separated between their other cards. Cutting the deck wouldn't change this as they were manipulated so they could draw a good hand of sufficient lands and other card types to play.
Technically the same thing could potentially be done in this game to give you a good selection of upgrades/cheap resource cards that could give you an early advantage. Its etiquette to offer a deck to be cut after you have shuffled but that player can still choose to randomise the cards further after a shuffle if they wanted to do so or if they suspected something. I certainly wouldn't ripple shuffle another persons deck and would also request if they wanted to randomise my deck further not to ripple shuffle mine. If I wanted to randomise someone's deck then I would deal them into several piles and pick each one up in a random order so nothing was damaged or bent. I would also suggest that the other player did something similar as an alternative to ripple shuffling my own deck.
Edited by scrozzers