Can anyone direct me to the statute(s) giving the Comptroller the authority to make policy regarding the collection of court costs that do not go into the state treasury, but are kept at the local level? I have looked in the Government Code and have not found it yet.

Many of the articles in CCP Chapter 102 refer to different statutes, the comptroller and the deposit and division of fees.

Try the comptroller's website. There's a link to local government assistance with all kinds of financial management sections for counties.
www.cpa.state.tx.us