Supposedly, you would only have to edit your pipeline to work with the new multi-texturing features. This isn’t hard to do: https://dpaste.com/AA63AVK2M.
However, this doesn’t entirely solve the problem. All objects drawn by the custom pipeline appear to partially reuse vertex data from the Texture Tint Pipeline (and nothing is rendered at all if there are no objects using the TTP). I haven’t managed to isolate the cause of this yet; as far as I can tell, all of the buffers are being bound and written to correctly. I suspect it may be a Phaser bug, but I may have just missed something in the shader. I’ll debug it more carefully later and report my findings.