I ran into a similar "problem" under a CGI server I run scripts on. It's annoying to have to use lib '/home/benizi/perllib'; and use lib '/home/benizi/perllib/site_perl';.

My work-around was to use the LIB parameter when compiling modules, rather than PREFIX.

perl Makefile.PL lib=/home/benizi/perllib

A lot of stuff still gets put into /home/benizi/perllib/sun4-solaris, but use lib 'DIR' takes care of that detail, adding both "DIR/sun4-solaris" and "DIR" to @INC. I also get errors about permissions when 'make install' tries to install documentation (the install location of man pages is unaffected by LIB), but they're (rightly) ignored in the process. And I don't do any of this manually: I set up CPAN to pass 'lib=/home/benizi/perllib' as 'makepl_arg'. (in a CPAN shell, type o conf makepl_arg "lib=/home/benizi/perllib")