You are free to use joomla's mod_mainmenu for mobile pages too.
Both mod_mj_iphone_menu and mod_mj_pda_menu are simplified version of mod_mainmenu with following features:
1. mod_mj_iphone_menu shows firstlevel items on homepage and subitems of current item on other pages.
2. mod_mj_pda_menu always show firstlevel items.

Hi!! i have the same problem, the only solution was to duplicate mainMenu, and assign a name like mobile_menu, then search in module manager the module mod_mj_iphone_menu that defines the principal menu to be used for the template iphone, edit and choose mobile_menu.

Then in settings for the iphone template, choose any homepage that you want.

So the solution is have 2 menus (1 for PC and 1 for Mobile), the top items from mobile_menu all have the link to the component search, i did it because all have submenus and if one of this have a link to article, dont show the submenus items.

Maybe there is a more elegant solution but for my proyect it works.. you can watch it in www.tsjqroo.gob.mx
greetings"!