We have recently switched from captive to CM for PCBs.   Most of our procedures were developed based on captive manufacturing, so there is a little adjusting to be done.

All of our SMT boards are documented as panels, to make sure that no matter who purchasing chose from our AVL, the boards came in ready to drop in the line.  Panelization parameteres were developed with manufacturing engineering.

I don't doubt that using those panels has caused our CMs to adjust.  Being minor adjustments, they aren't going to bother the customer.   I have had only one request to change a panel.  

We do require that all of our CMs, prototype and production, purchase from vendors on our AVL.  There are huge time and money savings in a known good vendor.  We have added vendors (after our approval process) on suggestion from our CMs.  For prototyping, we will often buy from our vendor and ship to the CM, to expedite the process.  Having a direct relationship with the fab vendor, not working third party through the CM, makes communication MUCH easier, and has saved us time and money by being able to implement advice form the fab engineers.  

It's the least expensive way to ensure quality PCB fabs, which we all know is a cost saving in itself.

Pete