Hi Emil,
Yes ,they both use mfgtool v2. The products of i.MX6 all are using the mfgtool v2 to download. And all IMX_MFG_TOOL_V2_SOURCE are the same. Dear Emil , I think you maybe make a mistake, the number of 4.1.0 is the version of BSP . Towards the "Mfgtools-Rel-3.0.0_121207_MX6DL_UPDATER" and "Mfgtools-Rel-4.1.0_130816_MX6Q_UPDATER" you have downloaded, the most differences are the files under the Profiles in Mfgtools.
Don't be confused, it's easy to decide.
If you are using i.MX6Q , you can go to http://www.freescale.com/webapp/sps/site/prod_summary.jsp?code=i.MX6Q&fpsp=1&tab=Design_Tools_Tab ,the related mfgtool is under Hardware Development Tools /Programmers.

If you are using other i.MX6 products ,the methods are the same.
Hope this can help you~~ Any questions are pleasure.
Best Regards,
Dan