Wow, didn't expect this to get so many replies, but I've learned a lot. For those wondering, yes, I have a military background, and I believe this scenario is likely common with military pilots, at least before the advent of the T-6 in pilot training.
I've learned a few things of my own here and by reading Part 61 again (several times) last night. I believe it took a while for my regulation-reading-comprehension to kick in. The FARs are more convoluted than most military regs, which is really saying something.
I've held a CPL-AMEL for a while, though I never exercised the privileges. All military pilot training graduates who want it can test for and receive a CPL-AMEL/Instruments without a PT (61.73).
61.165(e) allows me to get a SE ATP without any prior SE ratings as long as I meet the requirements specified in that paragraph (essentially 50 hrs SE + a PT) because I previously held an airplane commercial certificate.
61.63(c) allows me to add a SE CPL to my current ticket without a knowledge test or meeting specific time/training requirements by completing a PT with the areas of operations as specified in the Commercial PTS additional rating task table.
61.167(a)(1) allows an ATP certificate holder to exercise the same privileges as a person who holds a commercial pilot certificate with an instrument rating.
61.153(d) requires a commercial ticket to be eligible for any ATP. The only exceptions are for military pilots and foreign ATP holders. I interpret this to mean that no matter how hard you try, you can't avoid demonstrating commercial maneuvers on at least one checkride in your flying career. Personally, I've demonstrated energy maneuvers, including all of those required for a CPL, on at least seven different military checkrides in three airframes. Three of these checkrides occurred during pilot training, which (along with an instrument check) I imagine creates the foundation for getting a CPL right out of pilot training without a PT.
I asked AOPA this same question yesterday before all these replies were posted and they suggested simply adding the SE-ATP to avoid additional training/time requirements (though I don't believe those training/time requirements apply based on 61.63(c)).
That being said, I believe the CFI that instigated this post (again, not the CFI I'm currently working with, just another one I met) was incorrect and that I'm currently eligible to take the CPL-ASEL and the ATP-ASEL PTs. Haven't decided which route I'll go with yet, neither one really worries me that much, just want to reduce the pain to a minimum. Any suggestions? Did I misinterpret any of the references?