The ATT & BSD strands of UNIX diverged on features that were innovated like :
1) Reliable Signals
2) Virtual Memory
3) Shared Memory / Semaphores
6) TERMCAP & curses(3) (re-implemented by ATT as termlib with enhancements)
Given the widely perceived fragmentation of Linux distros, with tweaked features sets, for instance deb v rpm, it's naive to think you can write without regard to portability. Even with FHS, applications end up having to account for cosmetic differences between distros.
Portabiity is a requirement, otherwise you prevent change and innovation, and trust me you would not get much done stuck on Version 6 UNIX.
Look at the problems discussed with move to IPv6 last month!!! Portability allows the whole FOSS ecosystem to evolve and adapt.