That's what we've been told so far, they only want there to be 1 timeline because multiple timelines lead to war between the timelines.
But they also keep bringing up that there is a pre-planned series of events, pre-determined and dictated by the space lizards. The entire premise of the show is basically this. Loki was not suppose to pick up the tesseract because the space lizards did not dictate that it should happen, and by doing so a new timeline was created so Loki gets arrested by the time cops to be reset (a process they haven't exactly explained).
So it's just conjecture on my part. If the space lizard have said event A, B, C should occur but event X, Y, Z should not then there might be a reason behind it? If not, then the Thanos snap wouldn't be a problem because the Thanos span does not create multiple timelines, what would be a problem is the Avengers going back in time, so if the goal of the time cops was to only ensure a single timeline they should have arrested the Avengers in End Game, and sent them off to be processed by the ludicrously bureaucratic time cops. But they didn't because the Avengers time traveling was part of the plan (explicitly said in the episode) but Loki picking up a glowing box was not. Besides there is now two timelines at the end of End Game, at least, the original timeline where Captain America get's frozen and Peggy gets to die old and alone, and the new timeline where Cap goes back in time and secretly lives with Peggy and doesn't warn people about every single major disaster over the last 60 years (Hiroshima, Rwandan genocide, 9/11 etc.).