I just wanted to note, where you said, "at the end of the 1040, the amount of withholding from all sources (1099-R, SSA-1099, W-2, etc) will be applied to the tax," this isn't happening in the software. The 10% was taken out by my institution when my early disbursement was paid, but then an additional 10% was indicated as additional tax owed. At no point was the 10% already withheld applied to my taxes owed. I found a place to manually enter this into the software, but it took an hour long tech support call to figure out why (we never really did), and find what seemed like the correct place to list this.
