Beyond the flawed logic of the Catalyst, why was this never explained?

I never saw this as the intended theme but they did sorta make it more ambiguous after EC was made.

If what he tells you about organics and synthetics is true, then the choices as they're presented make sense as to why Destroy is bad, Control is okay and Synthesis is the main solution to the problem. This is what BioWare actually believed their ending was about when just Casey and Mac wrote it. They had forgotten the context of the prior narrative to create an isolated "meaningful" story as the ending or an artistic vision as they called it -- this was their message and the idea that Casey had in mind for the entire thing apparently.

Then think about the actual ending sequence for a sec. I know Shepard takes a breath in the high-EMS destroy ending, but that entire Jungle-planet sequence? That's solely directed in the way it is and ever was to showcase the ramification of Synthesis. It's Joker and EDI in the Garden of Eden playing Adam and Eve in a newly born world that get together to continue life in its newborn way.

Without that hug and that outlook over an almost dreamlike jungle planet with half-synthetic nature the scene is strangely empty and unresonanting.

Though, I believe the "dreamlike" qualities of the original ending was also BioWare's way of fading out what is canon and replacing it with what they believed to be a sort of vision about what the story could mean and that's why everything is suddenly so purely symbolic and you almost couldn't tell if anything was real or not from the moment Shepard goes up that floating beam-elevator right as you think he was about to die (and they removed the beam from the elevator in the EC btw). I sometimes think maybe Casey was just playing director. Mac wrote his draft for an end scenario and Casey told him to cut it down left and right until it became a properly "denoument"-feeling but without questioning how poorly the context of the scene matched the plot of the overall series, and that's where the original ending was so unsatisfying and confusing - it totally WAS a denoument when the Catalyst tells you it's all about organics and synthetics, as if to say that was what BioWare thought their story was about if you were to reduce it to its core element.