UPDATE for anyone who encounters this thread in the future...
I talked to a phone rep who agreed with my interpretation that the ES calculations don't make sense in my case, and she walked me through the steps to override the values in Forms view. Unfortunately, my attempts to fix things just made the ES numbers look farther away from correct, so clearly there's something else going on--that neither she nor I could figure out--about the way the forms are connected behind the scenes.
I decided that my best course of action would be to essentially start over. I put back the IRA deduction (to undo all the TT calculations in the amended return), and I deleted the overrides I had made, and then I removed the IRA deduction (again), so that TT would do a fresh calculation on the 1040-X. It still showed that I owe a payment with my amended return, and from what I've been able to learn about IRS rules, that's the way it is supposed to work. It's annoying to have to overpay, but I'll sleep better knowing that I won't owe an extra penalty at tax time next year.
As @fanfare points out, it's probably best to ignore the TT estimated tax calculations and just calculate yourself outside of the program. I'm annoyed that the answer to this glitch is to just DIY -- kind of defeats the purpose of paying for tax software in the first place -- but the great part (for Intuit) is that by the time you figure these things out, they already have your money! Oh well.
