in reply to Do I have to explicitly tell keys() that the hash in my hash of hashes is a hash?

In short, the answer is 'yes':
foreach my $customization (keys %{$servers{BOUVET}{customizations}}) {

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The long answer, and recommended reading, is perldoc perlref, perldsc, perllol, and perlreftut (the last one comes with 5.6 so is not on this site).
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In Section Seekers of Perl Wisdom