If your ruby
skills are good enough, you can probably catch this by changing
PREFIX/etc/pkgtools.conf to do the equivalent of `make -VINDEXFILE` when
the defaults for this variable are set.
Ideally, portupgrade would do that by itself. You are probably right in the
sense that portupgrade users should know their tool of choice better, but as
you can see in this thread, people only see that portupgrade's defaults now
cause INDEX rebuilds on every cvsup and nobody's blaming portupgrade for it.