'make install' can install binaries in one of two places based on the location from where it is invoked:
If invoked from the top-level dnssec-tools directory it installs files in /usr/local/bin; if invoked from the tools subdirectory, it installs files in /usr/
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Just call configure with:
--with-perl-build-args='INSTALLDIRS=vendor INSTALLVENDORARCH=/usr/share/perl5/ VENDORARCHEXP=/usr/share/perl5/ PREFIX=/usr'
Customize to suit your needs.