I admit to not being a PHP expert, but people who are have told me that when you use a code cache with PHP you hit similar scoping issues to the mod_perl ones. Otherwise, there would be no persistent database connections in PHP either.
PHP persistent database connections are handled by each database module itself and have nothing to do with code caching.
I believe that your informant is quite wrong about PHP scoping problems with code caching. Perhaps the person meant something related to stupid old bugs like this: Bug #5875 APC removes $_SERVER from global scope. Note the