Somebody at Xerox had PDF as a checkbox and put it into the scanner, and since Xerox is part of the JBIG committee, you can bet that they have free access to that and embedded that too....
Smaller files that are delivered in standard formats is a marketing/sales point. It's in a blurb from Xerox right here. The problem is that in implementing this feature, they don't have a particularly good way to turn it off. Maybe there is - I read through the user manual and system admin manual and I don't see anything that would appear to do that, although while it seems like there is templating system under the hood that could be manipulated into changing those settings, they didn't really go out of their way to document it.
It comes down to complicated choices that were informed by a marketing decision and hidden behind friendly menus that hide the complication.
plinth breaks down what you need to know about PDF compression, and what probably went wrong at Xerox.