Similar to Arduino, there is a pre-processor which converts the .ino into .cpp, generating the function declarations etc.
This can be found at: GitHub - particle-iot/buildpack-wiring-preprocessor: Overlay buildpack providing Arduino Wiring preprocessing
This is hard to answer in the sense that lots of files are used during the compile. But as a user, you can just think of it as all the files that you wrote will be uploaded to the 
for compilation.
Yup, Arduino is majority Atmel-based and Particle is on STM32xx which is why some hardware specific portions of a library will need to be reworked.