I was under the impression that the mod priority in the left window was akin to install order; whatever is later on the list gets put in the virtual folder MO creates and "overwrites"/merges with whatever came earlier. So wouldn't messing around with the left panel be the same as messing around with the installation order and therefore bad for STEP? I remember looking up an answer for this when I was installing the mods that said to not mess with it, but I can't seem to find the source at the moment. (not trying to be confrontational, just want to expand my knowledge of how skyrim/mod organizer works)
The conflict resolution order for some mods containing scripts differs from that of the corresponding esp. This may lead to subtle, hard to locate bugs. You should re-order the affected mods (left list!). There is no way to reliably know if each of these changes is absolutely necessary but its definitively safer. If someone suggested you ignore this message, please give them a proper slapping from me. Do not ignore this warning The following changes should prevent these kinds of errors:
Move When Vampires Attack after Even Better Quest Objectives
Move Traps Make Noise after When Vampires Attack
Move Thieves Guild Requirements - No Auto Quest Start Brynjolf after Traps Make Noise
Move Complete Crafting Overhaul Remade after Thieves Guild Requirements - No Auto Quest Start Brynjolf
Move Non-Essential Children after Complete Crafting Overhaul Remade
Move The Choice is Yours + Dawnguard after Non-Essential Children
Move The Paarthurnax Dilemma after The Choice is Yours + Dawnguard
Move Alternate Start - Live Another Life after The Paarthurnax Dilemma
Move Enhanced Blood Textures after Immersive NPC in the dark