Petalinux is brand name used by Xilinx, it is based on Yocto and pretty decent mainstream kernel, what Petalinux adds is the HSI (Hardware Software Interface from Vivado) and special tools for boot image creation.
Most settings can be changed with menu-config. There are 3 more files that user can edit, they are
|system-top.dts||Device tree changes are to be applied here|
|platform-top.h||U-boot changes are to be applied here|
|fsbl_hooks.c||FSBL changes are to be applied here|
There should be no reason to modify any other files by editing them (most of them are generated and would be overwritten).