Mostly for easier management on the files inside the archive (bsa). As you see on many occasions the guide asks you to remove or not to install some files that are contained inside the bsa and it's easier this way and not having to archive it back again.
I think this 80LootChanceNone [GLOB:28000D66] is what modifies the lvld chance none in skyrim esm and that is forwarded to the bashed patch from scarcity... plus author said quickchange is not required after the last update so i'm guessing that's the modification. Ofc i don't have that much knowledge in this and could be wrong.
I ran bashed patch without quickchange script and the bashed patch does not forward changes from scarcity. Many leveled items in scarcity have LVLD to 0 and the bashed patch forwards changes from Skyrim.esm edit: or this 80LootChanceNone [GLOB:28000D66] cancels the chance from LVLD ? edit2: i think it does. Let's try without the script
BCS patches are for other mods (not included in LOTD) that require books conflict resolving. Since BCS is included in LOTD and sirjesto already made a patch for CCOR - LOTD i don't think there is a need for a BCS - CCOR patch. EDIT: looked again in xEdit. There are 3 books edits by BCS - CCOR patch that are already included in the LOTD CCOR patch (now in LOTD Patches merge)
Well wrye bash (bashed patch) and the CR ( conflict resolution) are the most important things that you need to do or else due to conflicts your game wont work properly... as you experienced.