I'm assuming the menu is built in the primary (not master) script, so that the time callers take to make their menu choice is counted against the application service level. If you want to be consistent across your sites, you should build the menu in the voice mail system before the call is transferred (viz CDN) to the SCCS.
If you do not want to change scripting, you can estimate the average time callers are taking to navigate through the menu and add that to your service level threshold. So if you service level threshold is 20 seconds and it takes (on average) a caller 15 seconds to navigate the menu choices, you would adjust your service level to 35 seconds.
The first option is preferred as you will then have exact conformity across your call centers and you will not be making a "guess" as to the average time it takes to navigate the menu.