I think thats because a lot of extensions arent PPI compatible, and some that say they are usually miss something that doesnt get reset on bootup.
I really do love the hybrid mode, because anytime i need to go to stock, i just remove everything from /usr/local.
if u have a persistant local directory, in Appbrowser, all u need is select Download+Load.
But if for some reason an app doesnt work after rebooting, u may end up doing rm -rf /usr/local ; mkdir /usr/local/tce.installed