Flavor difference between marzipan and persipan
If you want to give something the flavor of almonds, then starting with almonds, in my opinion, is superior to starting with the cousin of almonds. Of course, if your persipan is, in your opinion, indistinguishable from marzipan, then go ahead and use it in good health, but it is likely that it has added flavors to get it to that point (natural or otherwise, depending on manufacturer).

Modern, sweet, cultivated almonds have a stronger almond-y (and in my opinion, better) flavor than apricot kernels and, I would presume, peach kernels (I haven't eaten those). 

Almonds, peaches and apricots are close relatives and the kernels are generally quite similar. Most peach and apricot kernels (as well as bitter almonds) are not edible in their fresh, raw state because they contain cyanide in the form of amygdalin. There are actually some apricots with kernels that are edible without extra processing and in my experience, they aren't as flavorful as almonds, although I guess there could be some varieties with more flavorful kernels, but I think the ones that are being used for the persipan are more likely to be leftover from fruit production and not a specific variety bred for the kernel itself.

When you make marzipan, you just need to grind up blanched almonds. When you make persipan, you need to process the kernels to remove toxic chemicals, which removes much of the bitterness, and then grind them up and probably add in some flavoring. 

I expect it is possible to get the persipan to approximate the flavor of marzipan, and I would expect the texture to be about right to begin with, but personally, I would say that yes, making marzipan from almonds is superior. It's using the variant of that particular nut-bearing tree that was bred throughout the centuries to make the flavor that this food item is most expected to highlight. Marzipan IS almond. ...and sugar, sure, fine, whatever. ;-)