Hi Doug
I bought this up last Nov 22 in this thread
New video by Michael; The Factory | Design A Product With Us Part 3: PCB Design In KiCAD
The short answer is no, I don’t think they will line up. Unfortunately this seems to be a universal problem and can be quite a nuisance. I think someone must have has some sleepless nights thinking up a way to make things as awkward as possible. I think there may be one or two manufacturers that align any pins AND the mounting holes on a standard 2.54 (0.1") PCB grid but it is very rare.
Cheers Bob
PS
The solution I have found is to mount the small board then connect the pin positions with a slightly smaller tinned copper wire so they can be bent half a hole to mate with your larger board holes. A nuisance but it is a neater solution than butchering boards to get the mounts to line up.