Let me ask you a question, since you're convinced that they can sound different.
Take a folder full of Word documents. ZIP it. Heck, re-ZIP it several times. Extract all the files. Do your Word documents look different? Did the formatting change? What about the letters? Did new words get inserted, or some others deleted?
We are not talking about a Word file. It does not have to be converted in the same way to convey timing information as well as content through various electronic devices to an electromechanical device. Regardless of your reasoning, my ears tell me different. I cannot explain it beyond that. I am not an expert in such matters by any stretch of the imagination. My friend did a rip via EAC to WAV and converted that rip to ALAC in iTunes. We compared that to a rip of the same tune directly via iTunes to ALAC. I can tell you with high certainty that on my system I could identify the files blindly 10/10 times. My friend felt the same way on his (very resolving) system. Yet in theory they should be bit-for-bit identical files. I can upload those two files should you care to compare them yourself and see if you agree, or you could try the same experiment if you have EAC and iTunes. On my office system, which is far less resolving, I could not tell the difference at all in the two files. There's plenty of discussions on similar topics on this and other sites. Choose whatever you'd like to believe, and use whatever works for you. I get your reasoning, and on face value it looks good on the page, but in real life, to my ears, it doesn't work that way. Enjoy the music!