I don't think it's deliberate RNG manipulation they worry about. It's a single player (or coop) game after all.

However, one of their design goals is that people playing on the same seed should have roughly the same game, it should feel "fair". Some things you probably want to be fairly random, for instance your card choices can depend on what cards you chose before. But it's also important that people choosing the exact same cards (and taking the same path, maybe?) should be offered the same options.

In STS1, the order of relics was fixed from the start as I recall. So if you skipped a shop, you'd get exactly the same relics in the next shop as you would have in the one you skipped. Good for seed fairness, but a little odd.