Yes.
To access scanner through TWAIN: http://asprise.com/product/jtwain/
and this will allow you to do ADF scanning in Java through WIA: http://asprise.com/product/jia
As you mentioned the second scanner has two functional units - flatbed and feeder, you need to select the second functional unit before calling ADF.
Disclaimer: I work for the company that offer the above mentioned products.