I knew the "make VAR=value" trick, and I use it wherever possible to avoid patching Makefiles (which is a maintenance nightmare). But it's not always useful.
For example, you may want to just change a part of the variable (i.e., to remove some flags), or you may want to append a value to it. Anyway, despite Makefiles were used to describe this technique, it is applicable to any other kind of file, such as configuration files, manual pages, scripts (as described in the #!/usr/bin/perl example), etc. Therefore, the same problems and solutions arise.
About the DESTDIR thing, yes, you are right. I'd have mentioned it, as it makes things nice with staged installations (and certainly helps some packaging systems). I forgot because we don't use it in pkgsrc ;)
Thanks for your comments.