- "If it's written with all the cross platform supported commands, then there are no api calls to worry about. "
Very doubful. The compiler uses OS specific APIs under the hood in interpreting (possibly not the best word) your code. if you use OS specific APIs in your code then you will break cross platform compatibility but sticking with PB code means "PB will use APIs based on the target OS" -NOT - "PB will not use APIs either"
File system. somewhat OS independant. When the OS is in design stages a file system (s) of some sort will be decided on for support if its purpose is to read and write to some form of media.
It sounds like you are getting OS design issues confused with what compilers do.
The OS boots the system, then it usually (but doesn't have to): loads some device drivers, provides and interface for communication, exposes an API for others to use.
The binaries that do this can be written in a hex editor on another system!
Excel macros can write binary files with anything in them so I guess excel could be used to write an OS
My point is that you are barking up the wrong tree,

"right tool for the job" If a dentist insisted on using a large hammer for every patient because it's a great hammer that's very expensive that he got for a good discount, (It could even be Thors hammer!) its still not necessarily the best tool for the job when his rich customers just want a polish