Oh, so I was right on the money about why Sidonia would be pissed at the MC for using purification magic on toilets: they make a fuckton of money and gain a shitload of power from being the only people to offer purification services, so him making a magic tool that does their job, but better, and so incredibly accessible even the common folk can afford it means he's destroying their power and funding without even really trying.
And, also, since this is 3 years (probably closer to 2 now) prior to when the other people get summoned, that throwaway joke about Sidonia starting a war over toilets is looking less and less like a joke every chapter.