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When using TWAIN, the printer makes no decision on filetype or structure, the application that is using TWAIN does that. So if you don't have a pdf option, it is the applications fault. Windows Fax and Scan as well as the new Win 10 one just called Scan both don't give pdf as an option.
Windows Picture viewer doesn't support mTIFF (multipage tiff) so you would need it in file per page format.
For mTIFF I suggest Irfanview
There are a plethora of free apps that do pdf, my suggestion (Mine, not Xerox's) would be NAPS2 because of the large community that helps support it, and it has a pretty robust feature set.
I work for Xerox, I have no relation to either application I list and don't support them in any way. I have never used Page Manager or even heard of it so I have no comment's on how it works.
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.
Does that mean your installed 6505 TWAIN driver does not have a feeder option in the profile as I showed above?