I'm surprised that a PCB manufacturer would make changes to a stencil, given that the required relationship between stencil aperture and component type is down to the assembly contractor and no-one else. Only they know how their own particular process works, what type of solder they're using, what reflow profile, what known issues from previous batches and so on. They're also the ones commercially responsible for the production yield; if a component doesn't solder properly, they're on the hook for the inspection and rework costs.
If a stencil needs changing it should always be at the request of the process engineer that will actually use it. Not the original PCB layout engineer, and certainly not on the whim of the company making the stencil.
My artwork has a standard note on the drill drawing layer which simply says :
APPROVAL IS REQUIRED FOR *ANY* CHANGE TO ARTWORK
It doesn't mean changes can't be made at all, it just means I must be informed about what is proposed and why before it can go ahead. If I submit the same job to two PCB suppliers, I expect to get back two sets of identical boards (and stencils).
There are other good reasons to be very particular about who gets to change PCB artwork and when. Some years ago I designed a PCB, we ordered a small number of prototypes, built them up, tested them, made some small changes, and ordered a much larger number of rev B boards.
They didn't work. Why? Because rev A contained a layout error which the PCB supplier had "helpfully" spotted and fixed without telling us, and which therefore hadn't been fixed on the rev B board. The PCB supplier, for whatever reason, didn't apply the same fix to rev B as they'd quietly applied to rev A.
Instead of the problem being confined to a small number of prototypes - which is why prototypes exist at all, of course - we now had a full production batch of boards that needed rework. The whole exercise was costly and time consuming.
Artwork changes: yes, if you need to, but TELL ME ABOUT THEM FIRST.