Wot you calling stock though, 1MB Falcon vs 2MB A1200?
The falcon was of course sold in three memory configs. To me it makes sense to count a 2meg fast/ 2 meg Chip A1200 as stock when facing off against a falcon. In both cases they're only using the intended memory slots the designer gave them, and both were sold like that new by dealers. What I'd say is not stock is when you start upgrading everything else - Atari never intended anyone to start hanging 060s off the thing. So nothing that fundamentally changes how it works.
I could also say that a 1MB Falcon is the slowest computer ever made, considering with a config like that it'd not be able to run anything worth turning it on. A 14MB one cost the same as a decent second hand car, so let's go with the 4MB as a reasonable example.
CT100 type of mods is another question entirely. If you have too much money there's the BlizzardPPC boards, and after a short wait of about 10 years longer than promised they even got out an OS release to support it properly.