I discovered to my displeasure using Redhat/Fedora that indeed some distros do tweak the source code you'll compile. This is more than just kernel configuration.
Hopefully the developers have made sure that your system won't fall over if you use the kernel.org kernels instead (they've probably not changed much, if anything), so you should get away with it. Back up your current kernel and try, at most you'll waste a bit of compile time and a reboot.
