In theory, if i rip WAV tracks using EAC w/ secure mode, and burn them to a cd-r with my favorite burning program <achew Nero 6 achew>, will it be as flawless as a retail cd straight out of the cellophane? This isn't a very important question but I and others have been curious for a while!

Only if you used offset correction. And cdrs tend not to last as long as an original...

Not necessarily. The error rate might be superior. Some burned CDRs are even not readable at all ("coasters"). It is very common to get copies as good as a retail CD (though it seems that nothing can be done about longevity), but it's quite difficult to prove that a given copy is.
K-Probe and Plextools pro are softwares that can measure the C1 error rate on CDs with certain drives. It saves the process of trying the CD on any crappy player you can think of until you find at last one broken one that would play one CD and not the other (that would be the effect of a different error rate in practice).

Oh ! And there is a lot of margin for error rate until ONE audio bit is changed between the original and the copy, because the error rate is measured on the raw CIRC data (level C1), not on the audio data.

The official specifications for audio CD and CDR are a BLER (C1 error rate) inferior to 220 per second averaged over 10 seconds, but also zero error in the audio data, after it is decoded by the CIRC decoder.

As long as your CDR met the specifications (no "coaster"), the data on the copy is exactly identical to the data on the original (the track markers might be offsetted by 1 or 2 100th of a second).

whoah! great responses guys! thank you very much pio!