Great suggestion, thank you. Their process seems to be a well-oiled machine with minimal communication, but there was a gap between placing the order and payment that I could request to see their production files.
Efficiency and automation is what enables competitive prices for a lot of those fabs. Unfortunately that implies less human eyes on the process, and so whenever something non-standard happens, there is a potential for problems. You can either give up on a faster lead time to gain opportunity to review & approve production files, or you can adapt your process such that it would fit their workflow better. Removing solder from BGA pads takes about 1 minute (including cleanup) for any half competent technician, so it might be actually easier for you to just do a cleanup yourself. Which is where I ultimately landed with my problematic IR-intolerant connectors - it takes me a minute to clean up the footprint, but if I was to request a production files review, it would add at least a day for a lead time (because of time zone difference).
Any idea what file format I should expect for their production files? Some kind of processed Gerber or something?
Yes, it's a bunch of gerber files, but when looking at them please remember that features size might be slightly different to what your original ones had because they applied their process-specific adjustments (like over-etching, and the fact that real traces have trapezoid profile as opposed to being a perfect rectangle), so you will typically see a bit wider traces and narrower spacings than originals, and that is normal.