I hadn't even considered the assembly, if that is something you are also outsourcing. You can't X-out one board out of the group without consequences. Perhaps the component cost for that board is negligible and you just allow the bad board to populate as dead waste, but then you have to communicate a different BOM requirement to the customer. Which is more human capital just to iron out stupid details. And in the end, you have to make up any odd missing boards... which means.. hrmm. Well, it gets sorta complicated, doesn't it? More likely, no x-outs is the easiest way to deal with it.
Instead of being able to parallel process 5 different panels through 5 lower cost machines, they will pile up in line for the more capable machine with the higher number of feeders. And you have to wait for parts for all 5 boards on hand before you can start.
Post assembly inspection is more difficult. Instead of parallel processing 5 different panels to 5 different workers who have to inspect 1/5th the data, you either need each worker inspecting all 5, or you have to have different workers handling the same panels 5 times.
Henry Ford figured out a lot of this stuff like 100 years ago. Maybe we are disconnected, just a little bit, to the actual process. Expecting multi-pcb panels at the same cost is just plain inconsiderate. Even if your boards are small, this costs when doing quantity.
Maybe first order wasn't big enough for them to care. But after many repeat orders they realize this is not a small order, just a spaced out large order.
I couldn't care less if I lost a few.
This requires enambiguous and precise communication which costs human capital (support/service). Failing that, misunderstanding and more human capital ensues.
I ordered a super tiny, simple board with assembly. I was surprised when they arrived each tiny miserable board individually bagged in static cage ziplock bag. (There were no semiconductors on the board, even.) I didn't really think about it at the time of order, but I expected something like 100 per bag. Or even just a box with all 3000 of them. It was a PITA to open each one, and it cost them money. But failing the ability to read minds, it is probably less costly in the end to stick with the program if in any doubt. The customer can't complain for getting consistent service as agreed upon. And stopping to inquire can cause more damage than helping. If the customer is not expecting communication and doesn't answer immediately, there can be delay that can cause problems on both ends.
That said, of course if I'm Rx8, I'm unhappy at this price hike. And compared to one single board, it probably does not cost more. Maybe it's just the opportunity cost. Like any business, there are more and less profitable services. And maybe even loss-leaders that are suffered in order to get the good business. Say you sell hotdogs at 200% profit margin and hamburgers at 0%, and someone orders 1000 hotdogs... but with stipulations that financially turn them into hamburgers.