About patch in Cycling74's website

What is that XY object, Javascript?

looks like an older-looking version of the 'pictslider' object... or, it could also be 'pictslider' with their own custom 'jspainter' file loaded into it(see the inspector for 'pictslider'... and i can't remember where, but there's examples of 'jspainter' scripts to alter the look of various UI objects somewhere, perhaps on this forum)... then again, it registers when you click down in a way that seems less like 'pictslider' so perhaps it is a custom jsui(?)... but you can start with 'pictslider' to create your own.

And what's in [p scaling]?

it's probably similar to what you see on the left-hand patch with the 'scale' object: the 'pictslider' object defaults to have 0 and 127 be the X and Y range, so they're just scaling those numbers within a more interesting range for the 'simpleFM~' abstraction and the frequency of the amplitude-modulating phasor~... you can instantiate 'simpleFM~' and try that on your own(more fun to cater it to your own ears/liking), but here's my guess as to the amplitude-modulating phasor~ frequency-range:

Also, what's the purpose of [atan~] before the output? Is it like a limiter technique?

sort of... more like a 'saturation' technique... as a signal is pushed more into a curvy portion of an S-shaped waveshaper(sometimes also known as a 'sigmoid'), natural harmonics are emphasized more in the resultant distortion(atan~ is one such S-shaped/waveshaper-like function).
to my ears, more often than not, this is used particularly to fatten a synth sound(gives it more body and presence despite a limited amount of headroom).
it does also have a limiting effect, but not as exact/predictable in the same way as a dedicated limiter(limi~ would be better for a trusty limiter at the end of your patch).

hope it helps 🍶