AIUI Two fids are standard, but most subcontractors ask for 3 to detect a board inserted the wrong way round.
If your PCB is so warped it needs more than 2 fids then you probably have bigger problems to worry about.
that's the smallest side-effect that you can detect if the board is right or not. Their software is very likely doing some affine transformation.
Two fiducials cannot do that as you might know. The warpage of pcbs doesn't need to be extreme, small warpage can already cause some issues with some machines, so they won't detect the fiducials properly anymore (strictly pointing at Mechatronika at that point).
Warpage itself is not a big deal if you know how to deal with it properly. With lower quality TG material it can be a common problem after reflowing one side of a double sided PCBs.
Mechatronika is also only using two fiducials, I used this for a few years and went to affine transformation .. and never looked back.
Since their software was such an epic failure with our components we rewrote the software and things evolved step by step.
The machine is not being used anymore but we built another one in Taiwan (with all the knowledge we collected over the years).