As far as I know, it's not supposed to work if
grep DESTDIR Makefile
returned nothing, but in some cases I have had it work.
There are a couple things you could do if it doesn't work. You could set an odd prefix when building the stuff (like /usr/local/MYINSTALL), install it, copy the tree to the plce where you are building your ipk, move the data from /usr/local/MYINSTALL to /usr, then edit the packageconfig file (packagename.pc, I believe) and change the prefix there. It should work then.
I asked the same question a while back, and Meanie had some good info. Look for a thread with "destdir" in the name, and you should find it.
Hope that helps.