I know this is an older forum but I have emailed Santa Curz this week about this question and this is their response.
Michae M. (Santa Cruz Bicycles)
Jun 26, 12:18 PM PDT
Hey Brad,
You are welcome to paint the frame (we definitely recommend taking it to a professional for highest quality results) and it will not void your warranty. However, if any issues or damage arise as a result of the paint, we won't be able to support that through the lifetime guarantee. The warranty will still cover you for any manufacturer's defects and you will still be eligible for no-fault crash replacements as well.
Let us know if we can answer any other questions for you. Thanks for reaching out,