[JHolland]

Its just a front end, a bit like a glorified text editor, it still uses Arduino so it makes no difference to the compilation, compared to using the Arduino IDE; the only issue is if it uses a different version of Arduino which could could use a different version of avr-gcc.
Atmel Studio is another matter, I noticed that in the latest version the source files have a cpp extension which implies that its cpp code, however, on examination its still Arduino, so there is no chance of it building.

[jonbill]

i don't know if both use the same compiler underneath, but they have the opportunity to use different compiler settings and dependency handlings. Its not just about editor preferences.