Hi Bernhard (SAP Upgrade Expert 
),
Thank you for the information.
Please find below the details:
1> Shall i assume that Step 2A output is a new feature with SAP NW 7.31?
2> I went through note 1539556, section A (Complete missing modification flags in SU24 data).
Just to inform you, the Sandbox system (new release) is a copy of test system (old release). Now, I did a quick check in tables USOBX_CD for 1 standard sap tcode which was changed from sap defaults in DEV & TEST systems old release. I found that USOBX_CD table showed 2 entries for this tcode in DEV system while in TEST system it didn't. Do you think this may be the issue for wrong output in Sandbox system (new release)?
3> Also, if this is the case, do I need to run section A i.e. SU24_AUTO_REPAIR in my DEV system (with new release) before I start SU25?
Couple of other observations:
1> Though Step 2B did not throw me the list of standard SAP tcodes which were modified in earlier release, SAP itself has taken the sap new proposals + custom changes for such tcodes. I went to SU24 and confirmed this. Also changed their check indicators to sap defaults.
2>I think 2B output was incorrect compared to earlier release, but still the 2C roles were correctly populated, with auth objects added / removed as per SAP proposals.
Appreciate your help on the below as well:
1> Say I ran 2A, 2B; identified that some SAP std tcodes were not available in 2B output hence modified those using SU24 immediately and the data is saved in a workbench TR, 2C and 2D completed. Now i execute Step 3 which carries complete data from tables USOBX_C & USOBT_X (I assume that in step3 it will ask for a workbench TR).
My question: SU25 -> step 3 will also take the changes which I made using SU24 (for which a TR was raised) or I need to first transport Step3 followed by SU24 changes, followed by 2C role changes.
Thanks,
Sunny Doshi