yeah, it's a cost thing, nothing more, and as others have noted, it's really nothing new, home hardware has been used in arcades all the time.
back in the day it was possible to get the better over another manufacturer by doing things your own way, using your own hardware, throwing as much of it in there as you could.
these days it's not cost effective to do that; you're probably developing on a PC and want to be able to port what you've created to other platforms as easily as possible in most cases (large full-scale attractions excluded) also working with standard platforms means there's a good pool of developers to hire from too, rather than having to train them all to work with custom cases.
as I already said, it's not really surprising, even before the boards simply became PC boards you were seeing off-the-shelf PC cards used, look at the Golden Tee Fore! hardware, it might not be x86 based, but it's still quite PC-like in many senses, and even earlier the likes of Taito were experimenting using a standard PC motherboard but coupled with custom cards containing all the game roms and video+sound hardware (Psychic Force 2012) The x86 processors were a huge leap from what you traditionally saw used on arcade boards, which is also why there's a leap in the emulation requirements if you want to do it all properly.
it's not just arcades either, look at the current gen Sony / Microsoft platforms, they're borrowing heavily from the PC side of things (but are different enough that you can't just hack the code to run.
it wouldn't surprise me if we see some of the smaller manufacturers switching over to lower-cost boards like the R-Pi once there are ones on the market that meet their graphical needs, or can be paired with a PC video card; I'm a little surprised we're not seeing this for non-video redemption machines already but it's possible the devices available don't offer the number of IO ports that would be needed without further expansion either.
but I'll reiterate my original point, it's still a PCB, just one you're more familiar with. ultimately if we're doing proper emulation, it still needs emulating as a PCB, not simply hacking the code to run on Windows.