Some theories are of course only theories because they have yet to be proven, other things are no longer theories because they have been proved. Good luck with disproving the laws of physics...
As for the question you had asked avout marvelling at CDs when they first came out, my first experience was walking through some large shop or other, might have been a department store or a supermarket, hearing one playing and thinking it sounded pretty good, very clear sound - i.e initially impressive, but the wrong environment to really marvel. Not long after that, my brother bought a player (no idea what - nothing particularly hi fi, but then they were all supposed to sound great) My first reaction hearing it in his house, compared to records: yes, pretty good clarity, no surface noise, and very good dynamic range - it would have been something to marvel over ...except that It sounded harsh, and there was no bass. Not good.
Time passed, and many hifi mag reviews read, and by mid 80s the impression was that things had improved a lot, so I went to a hifi shop to try. Much less harshness, actually not bad ...but still no real bass. Not something I could live with. It was not until 1990 or so that I heard a player that did actually sound good, with at last the benefits shining through without the major limitations, so I bought into CD. But CDs recorded even in the early 80s sounded good on it, and music ripped from them still does. So, it was not the digitising, nor the file format nor the physical medium that was the limitation, but the players.
The parallel between that and now, is that lossless formats are all fine and interchangeable, but the player has to be able to play it well.
You may have suspicions that file formats can't be transcoded without detriment to sound quality, but until you do something to prove it, they will be just that, unfounded suspicions, which like, say, human jealosy, can ruin the pursuit of music. So I suggest going and doing detailed tests and research, to try to find find some real evidence that something is amiss - and if you can't, stop beating yourself and others up over it.