“Once” came from the word “ones” which is genitive of “one” which, of course, means a single thing or person. In the case of “at once” it seems to mean “now” because of this association with singularity (not that Singularity!), a single moment in time, which could be past (Once I had a chicken sandwich…) or in the case of “at once”, NOW. I suspect that the phrase used to be “at this once” but the word “this” was dropped, making the meaning less clear. Think of the phrase “just this once” where “once” is used in the same sense, except more clearly because “this” is still present to tell us which once!