As far as I know the adf should work fine with all applications. You probably will need to contact Xerox and speak with the 2nd level group where it is not.
Xerox has a partnership with Nuance so I'm sure they would suggest them if asked. From a Xerox standpoint scanning to a folder by SMB or FTP is by far the better option since you can make all the choices yourself. Scan by USB forces the lesser TWAIN (or WIA) to be used due to the protocol limitations.
And it isn't my product, I've never seen or used one in my life, I am not the company, just an employee that helps people on my free time. The only way you are going to interact officially with Xerox is through calling them direct so you can get to an employee that actually has the product on hand.
This forum is for customers to help each other out, any Xerox employee interaction is by their choosing. It's the first sentence at the top of the forum.
I did find one on the Xerox LAN and installed it via WIA/TWAIN over the LAN (So not USB like yours) and do have the option to choose the ADF. So I did a scan choosing the glass and got a single white page scan in pdf format (expected since there is nothing on the glass to copy)
Then chose the Feeder and instantly got faulted since there is nothing in the feeder to use (Which I assume to be correct, but can't verify since I am in Saint John NB Canada and as far as I can tell, the printer is in Webster NY USA.
So I can say that the TWAIN driver is absolutely capable of using the document feeder for scans.
I can do so in Win 7 x86 and Win 7 x64.
I did not test Win 8-10 or OSX.
TWAIN works in profiles (preferences) though, it is starting to sound like you haven't looked at the profile on the PC since you see no option to even choose the feeder.
In NAPS2 I can just select Profiles and change those settings at will, if your application of preference does not then you likely need to change them at the OS level as shown above.