As you know, the script 'rake build:iphone:setup_xcode_project' copies the content of the app and place it in to Rhomobile gem folders. If you can hack that or override that script a bit then it may do the thing you are asking for.
Thank you for your suggestion Kutir Mobility.
I have been able to hijack the script successfully. Here are steps
1. Create a hijack ruby script that contains
namespace "build" do
namespace "iphone" do
task :setup_xcode_project => ["config:iphone"] do
In fact, you should copy the original code from gems.
2. Modify the task definition at step 1
3. Load the hijack ruby at the end of the file
4. Now your definition will be invoked instead of the original method
5. To add framework, I was using the kronenthaler/mod-pbxproj · GitHub