TES4Edit only loads those dependencies when the mod has them listed as masters. Part of why the advice is to just leave patches alone because they don't always have every master specified. Some patches have none at all and could end up being mistakenly processed as dirty edits when they aren't.
So I assume 'patch' would consist of UL patches, OCC patches, BC patches, or just about any other mod patch out there?
EDIT: Here is the list of mods that ended up requiring cleaning...
Francesco's Leveled Creatures-Items Mod.esm
Francesco's Optional New Items Add-On.esm
Oscuro's_Oblivion_Overhaul.esm
Mart's Monster Mod.esm
Toaster Says Share v3.esm
Colourwheels sixy Female NPCs.esp
xeoex.esp
Francesco's Optional Chance of Stronger Enemies.esp
All Natural - SI.esp
Killtastic! Toggle.esp
QQuix - Rock, rock, rock your ship - V3.esp
DLCMehrunesRazor.esp
DLCSpellTomes.esp
Colourwheels sixy Stock Armor & Clothing Replacer.esp
Slof's Horses Base.esp
Bob's Armory Oblivion.esp
Oscuro's_Oblivion_Overhaul.esp
OBSE-Storms & Sound SI.esp
OOO-No_Guild_Ownership.esp.backup
Oblivion WarCry EV.esp
ImpeREAL Empire - Unique Castles - All The Castles - Merged.esp
Kvatch Rebuilt.esp
DLCFrostcrag.esp
Knights.esp
M.O.E. - Main Quest Delayer.esp
ShippingInCyrodiil_Normal_Lights_V1-1 - With Drawbridges.esp
MidasSpells.esp
Personality Idles - Modified version.espDeadlyReflex 6 - Combat Moves.esp
EDIT: It's advised not to clean Personality Idles- Modified version.esp - I experienced issues after doing this. Stuck animations etc...