> Double-$ should work. What makes you think it doesn't?
Huh, I tried it again and it worked (not sure what I was doing wrong before)...
$ ./configure.py -g ninja nvptx--nvidiacl
$ sed -i 's/\$(DESTDIR)/$${DESTDIR}/g' build.ninja
$ ninja
$ DESTDIR=xxx ninja
$ ls xxx/
usr
I'll take a look and see if there's an obvious way to patch this.