Justin, this really comes down to a question of what you need to charge to make it worthwhile (profitable) for you to do the job. The difference between ordering a non-slotted vs. slotted board is often in the $10-$20 dollar range. But if these were available at that price I am sure your customer would go that route. If you are going to spend an hour (or two) between coordinating with the customer, ordering the fretboards, setting up the tablesaw, spending time considering the best orientation, measuring twice, coordinating with the customer again to pick them up and pay, then that price point doesn’t make sense. I would try to make an estimate of time involved and multiply that by your hourly shop rate and then tell the customer, “this is what I need to charge to do this job.” Doug Proper has some excellent videos in the archive on determining shop rates and profitability. And while it is easy to say, I , and just about everyone I know struggles with this exact thing.
It is much better to quote high and charge less. Another thing to remember is that if you do it at a price that is not sustainable for you, the customer will often come back in the future for the same job expecting the same price. Obviously you are not bound by that price but it does make for an uncomfortable interaction. I hope that helps,
Jamie