Hi Narpal,
#1. I don't think there is such limitation, as far I know you can have both running on the same machine (EP/NWDI)
#2. Biller Direct does not need to run under anything 'SAP' branded, you can extract and run it locally in a Tomcat if you want, -- also, there is no real need for NWDS as far I'm aware.
#3. Since you don't need a bloated AS like NetWeaver to develop, you can just use a Tomcat or Jetty Container pointing directly to the root folder - you would have 'instant' access to modifications, (change in eclipse, save and hit f5 in the browser)
SISU has a paper for this (I used to work with those folks) and I can guarantee you this way is at least 1000x better to work than using NWAS, NWDS and NWDI.
http://www.sisusoftware.com/assets/Uploads/E-Commerce%20setup.pdf
Hope it helps,
D.
PS: we are talking about Java here, and there is no bloody way SAP can be restrictive using such language.. so be aware of 'not possible' answers, they are usually possible.
PS2: leaving the 'SAP Stack' you are also free of 'SAP Limitations' and they are quite A LOT.. removing NWDI out of the equation will bring you a solution for a problem you also mentioned in this thread.