I thought I would share with you how I solved the problem of the iPhone displaying the MAINMENU as the homepage... (note - my issue with the homepage for you latest alpha build is unresolved)
1. Edit the index.php of the iPhone template to match the homepage I assigned to the iPhone in the component
2. Create a menu specifically for the iPhone
3. Set that new, iPhone-specific menu as the choice in the mod_mj_phone_menu
Since I wasn't using the breadcrumbs/pathway, the HOME link in the path didnt affect me.
Given that i was able to get around that silly iPhone issue, Im sure you guys can work it out too.