Yup, I understand, completely. One of the things I noticed when using BS for a 15bbl system was that the relatively small errors in homebrew batches were amplified to a barrel or so at commercial scale.
Here are a couple of reasons:
Commercially milled grain retains less water than the coarser milled homebrew size. This adds to the volume of your first runnings and the symptom is inexplicably lower first wort gravity than you'd expect. Roughly, the percentage of lower gravity corresponds to the higher volume of free water. You can change this in Options.
Expansion is more apparent in commercial brewing. I found that a setting of 3.15% shrinkage corresponded more closely to the difference between 70F water and 180F water. I don't measure too much at 212 and my beer isn't 34F until I crash it. That means less difference in shrinkage. This can make a barrel of difference.
WHEN you measure your volumes makes a difference. Be consistent. I stop my sparge based on a 200F reading and where the gravity is. I measure my pre-boil gravity at 10 minutes after hitting 211 degrees. This is because that's how long the first hot break takes to lose foam without foam control (which I use to prevent boil over) and because that's how long it takes for the kettle to mix itself. I've always counted the start of the boil as when the first hot break crashes but I don't see it with the foam control, thus the timing.
I measure post boil volume after WP and settling. The kettle temp is close to 190F, which is in line with the shrinkage value I noted. I WP longer for highly hopped beers to gain more aroma, so it averages out to just above the 180F of the shrinkage percentage.
If you are sparging out to tailings, I recommend that you stop sparge water when you reach 6 plato. That's just about right on most systems to finish at just above 2P.
Check to make sure that your yield to the fermenter is accurate. Use hot water that you run through the heat exchanger into a fermenter. Then make sure that your brewhouse efficiency matches your measurement to the fermenter. Just a few percentage points can make all the difference.
Lastly, don't assume all your recipes will have the same brewhouse results. Have a baseline, but change the master recipe equipment profile to match your results. There's a vast difference between my Pilsner and my DIPA in terms of yield. I have three baseline equipment profiles, based on gravity range and kettle hopping.