[Andreas]

If you take a look at table datastore for record pluginlist you will find smth. linke this:

a:1:{s:12:"global_start";s:32:"// some code for hook global.php"}

This is a serialized array.
Upon execution it will be unserialized:

PHP Code:

$pluginlist['global_start'] = '// Some code for global.php'; 


Then this code will be executed:

PHP Code:

eval($pluginlist['global_start']); 


Variable collisions are always possible.
As this unserializing and evaluating is being done at execution time it generates overhead. So for larger code modifications you might want to use include files - then less code must be unserailized and evaled.
Include files can also be pre-compiled/cached -> eAccelerator/ZEND Performance Suite/etc.