You can calculate how much money you save for each hour of commute:
(700 CHF/month) / (40 minutes/day * 15 days/month) = 700 CHF / 10 hours = 70 CHF/hour
You can ask yourself: is this a sufficient compensation for my lost time? You can optimize the time spent on the commute/rationalize it (I will read a book, listen to podcasts, take a nap) and I suppose that too often people go for the money.
Also, since one flat is more expensive, is it also not in a cooler place where there is more going on to keep you entertained? Is the cheaper flat at least in a quiet place near nature, or just some generic sad swiss town?