The correct caveat for this case is actually a little further down under the "Problems with Scripts Running with Registry Handlers that Cache the Code" heading. In particular, "cached code won't run 'use My::Utils;' again". Similarly, "use base ..." doesn't get run again therefore base::import doesn't initialize @...::ISA again.

A solution (as mentioned) is to not do such things at compile-time. Instead use, for example:

require base;
base->import( qw< ... > );
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Of course, not having such stuff initialized at compile-time might break code structured in unfortunate ways, so test it.