Let's say I want to take a live USB with persistence, boot into it, get it all setup then install it. Will all my features still be there?
If not, is there a way to do this?
No. The UsB Persistence, does make changes and keeps them only for the Live instance. In some cases, further modification is required to enable things like graphical card settings and network card settings to be saved. In other cases, system wide updates do not work.
To make permanent changes to your Live USB you should use RemastrerSys For example you can :