Many ./configure scripts compile small test programs or run scripts check for other system info (e.g. uname -a) and get incorrect info. It can take sometime to get it all working. I'd rather ./configure on the native platform (arm in this case) and make and go to sleep. Some very large projects (like expect) fail not allowing a cross compile in ./configure.
Absolutely; it's just a matter of deciding whether it'll take longer to alter the configure script by hand (setting variables to what you know they should be, running some snippets on the Z to find out what, etc.) and then compile on a quick machine, than to run the whole lot on the Z.
Sometimes I do think that I'd go the Z route, but it's far quicker IMO to edit the configure script.
That said, I'm still having troubles with R 1.9.0 (lack of time to alter configure mainly) so if anyone knows that one of these on-board compilers comes with F77 and is GCC3.xx then I may give it a go (I know there's another full featured compiler which meets these requirements from a Japanese web site, but again, I've not had time).