Coming from personal experience.
Someone needs to authorize the work to be done. So if theres a slight chance warranty claims will be denied, the customer needs to authorize the estimated job. If in fact its a warranty issue then the customer is not charged. Now if in fact it was caused by aftermarket product or outside source. Then it is put in writing, explained to the customer then he is billed. Now if the customer does not want to authorize thee work (sign the RO) he is then turned away. Dealers are indipendent of manufacturer. So warranty claims has to be approved, and if denied dealer eats the repair if not authorized by the customer.
Even on our comebacks,we have customer sign a 1 hr diag. We just take the time to explain to them whats going on.
Just keep in mind once all said and done, if it is caused by aftermarket parts. Then get evrything on the invoice, with explanation on how and why. Save all parts. Pay extra if you have too. You can go after the aftermarket shop. You can probably file a claim on your insurance and they may help you go after them.
If it is warranty, and you spend extra money for tow and remove the aftermarket parts. As long as its stated on the RO that the dealer wanted you to do this before any further diag. Then you could try and more likelly get it reimbursed from warranty claims.
Buttom line get everything in detailed writings. You should be covered either way.