I hate to bring back one of the disputes as old as dirt (in the Free Col default graphic set) but I just tried a network game yesterday and trying to build a colony on Apache land (b) I received a warning similar to the one you get when you put a colonist onto a plot owned by Natives.
This isn't old Col behavior, it's C4C behavior. But to be frank, I'm not sure whether or not this action would cause any alarm in the native population in the original game - I can only assum it would nott, since there was no warning, and you usually ended up surrounded with nat. territories anyway. If it does cause alarm, then this is just a useful feature and a fix of original Col's glitch. But then again - I'm not sure if you made this change on purpose... .