I’ve got both Atlas and Peco machines, code 100, on my HO layout. I’ve also just installed some Peco switch machines under some old Shinohara 3-way turnouts.
NEITHER of these turnouts/switch machine combinations contains the extra contacts for signals or indicators. (For the Atlas, I’m using the standard surface-mount snap-switch motors.) Both are AC/DC powered twin-coil systems. From my experience, both of them work a lot better with a capacitive discharge circuit than with straight transformer power.
Atlas does make an under-the-table mount, but it only has about a 1-inch, maybe 1.5-inch, shaft. The machine itself must be mounted horizontally, and it’s a good 4-5 inches long. With this short shaft, it can not be mounted beneath a 2-inch foam layout without a lot of hollowing out. It seems to be designed for 3/4-inch plywood with roadbed, and nothing thicker.
The Peco system connects the points to the switch machine with a rigid bar linkage. Atlas uses a thin springy wire. To manually throw the Atlas, you need to puhe little lever built-in to the top of the machine. To manually throw the Peco, you can just puhe points over and the switch machine will follow. The idea of inverting the Atlas machine is interesting, but if you do that, you will not be able to manually throw the turnout - it will be electrical-throw only. Likewise,the Atlas below-the-table can not be thrown except with power.
The Peco switch motors fasten solidly to the bottom of the Peco turnouts. This makes alignment a non-issue, and provides a very solid throw every time.
If it were not for the cost, I’d use all Pecos. They really are that much better. Still, I can’t complain about my Atlas turnouts. In fact, I have a lot of old brass-track snap switches from the 60’s. I’ve bought manual snap switches in NS for my layout, and I am re-using the 40-year-old switch machines. They’re free, “pre-weathered,” and I haven’t found a bad one yet.