I haven’t tried swapping Atlas TO’s with Peco’s,so I can’t honestly tell you how accurate your informations are.However,the theory for TO numbering is based on the distance of diversion vs the forward distance,meaning that,for instance,a no.4 TO should have a lateral movement of 1 in. for every 4 ins. of forward travel while a no.6 TO will require 6 ins. of forward travel for an inch of diverting.This means that the diverting angles will obviously be different also making pretty hard to substitute them,often at the price of major modifications to the adjacent trackwork and scenery.
But since TO manufacturers tend to have their own way of designing and identifying their products (ex:Atlas give numbers to their TO’s while Peco call them small,medium and large),it becomes pretty much a trial and error task to interchange them,and if you’re lucky,without too much work.
Your assumptions are not exactly correct, unfortunately. The PECO N scale turnouts are built differently from the Atlas turnouts. That is why they are named “Small, Medium, Large” instead of #4, #6, etc. There are also differemces in geometry between the PECO Code 55 and the PECO Code 80 turnouts.
Peco Code 55 small, medium large all use a #6 frog. The difference is in the radius of the diverging curve. Small, 12"R, Med. 18"R, Lrge 36"R.
Peco Code 80 medium are a #4 frog with 18" R diverging leg, Large are a #7 with a 36"R diverging leg. Some people call the PECO Code 80 “Setrack” turnout a small, but it is very tight … soemthing like a #3 frog and 9"R diverging curve.
The one place you are in luck is that the PECO turnouts are pretty compact, so you may be able to fit them in … but it could take some fiddling.
You should also be aware that some PECO turnouts are wired differently than your Atlas turnouts. If you are using the traditional Atlas N scale turnouts, they probably have a “dead” frog. PECO Code 55 come only with a live frog (“ElectroFrog”) and PECO Code 80 come in a choice of lice of dead frog (“Insulfrog”).