Not sure how the maths works out, but I suspect they wouldn't be doing it if it wasn't a clever way to make a few (hundred thousands of) CHF.
Haven't seen this approach being taken at any other stores as yet - have you?
Edit: Actually, as I flick back through bank statements, I see all charges on my credit card statements right back to 2015 end in either a 0 or 5 - clearly I've been operating with blinkers on for years!
Over the life of your car you can save a fortune by always buying to the nn.02 of petrol/gas. That will always be rounded down to nn.00.
.01-.02 rounds down to .00
.03-.07 rounds to .05
.08-.09 rounds up to .10
Swings and round-abouts.
The total must be rounded down to an amount that can be paid with the available currency/coins. Reason being that rounding up would break one or more of the offers you accepted when buying that thing for x.yz CHF.
This came into effect with the devaluation of the 1-Rappen coins sometime in the later naughts, up until then it was possible to pay without rounding. It may have taken some time for the retailers to implement this, it wouldn't surprise me if they originally rounded up amounts of 3-4-8-9 Rappen. However even these rounding-ups probably led to a net zero outcome as rounding down would have happened roughly equally often and by equal amounts.
When paying electronically there's no need to round, your bank will happily accept non-rounded amounts.