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Look up a guide on how to do it right and you'll save yourself a ton of headaches.
Blindly merging does nothing to "help solve" conflicts. Sure, it gets rid of them - but not in any sensible way. It's a diceroll, and is ancient modding mythology from years past, at least in the sense that everyone should do it just to save some plugin space.
Every single modern modding guide does not recommend bashed patches for NV because it's a spectacularly bad idea for an average user. If you know enough to safely merge plugins, you know enough to patch manually and not need to.
NV's 140 plugin limit has been patched, and additional plugins does not impact load times or stability in any measurable way. The only time merging makes sense is literally if you're at 255 plugins - and in that case, *most* average users are going to have a broken game anyway.
If you really want to get into real conflict management (not guesswork done at near random), learn The Method[tes5edit.github.io] first so you actually know what is being done. After you learn it, then you can make the educated decision to merge automatically - or more often, manually patch instead.
The universal mantra of "always make bashed patches" goes back to the era when people recommended "always clean vanilla esms" and all other manner of unnecessary and potentially harmful practices.
It's one thing to go back to a familiar mod manager - that makes sense. It doesn't make sense to recommend an archaic - and more importantly, destructive - mod manager to new modders. MO2's strength is that - especially since they added Root Builder - it's completely virtualized and impossible to change or break vanilla files. Even Vortex is generally safer for a new user (although load order management is bollocks).
As to the original questions - LOD generation is the last step. Make sure you do not generate LOD into the base game folder. Generate it into a separate folder and install like any other mod.
Many people don't think of Wrye bash as 'archaic.' In fact, you can do many, many things with it, safely that no other mod manager supports. And it's still being supported. Before you call it archaic, go read the manual.
As far as MO2 goes - it almost crashed my PC. Why? Because, in-spite of being installed on E: drive - it put tons of 'administrative crap' on C: without telling me. Took all the storage space, which then blocked Win 7 from paging. For such a non-archaic mod organizer, MO2 should automatically not touch the c: (OS) drive unless user actually clicks something permit it. I now use MO2 for skyrim. But older Beth games, Wyre Smash/bash is the way to go. So many functions. Save game fixes, merged leveled lists, install/uninstall mesh/textures with one click, color coded status of mods in relation to current order, color coded health of save games, function to reorder mods to match an older save game you want to use. And more. SO many tools ... All MO really has going for it is the 'virtual' aspect.
Never confuse "new" with "improved." It ain't always so.
If you want to apply archaic to Wyre - I mean, you do imply that with the phrase "older Beth games" yourself.
As to the part about MO2 - that's what an *installer* does in Windows. Any installer that conforms to how Windows dictates an installer should is going to make registry changes and add dependencies to your system folders. That's literally how they are supposed to work. That's why they show up nice and pretty in Add/Remove Programs.
The nice thing is that MO2 also has a portable installation system that makes zero changes to the host PC and is, as the name suggests, fully portable without installation. That's the recommended usage, in fact. Maybe... how to phrase this... "go read the manual."?
As to the rest of it, save game fixes break NV saves. The color coded "save health" system is guesswork based on nothing relevant. It doesn't save enough metadata to correctly recreate a modlist for an older save game - it gets close, but it can still frequently fail unless you've kept manual notes.
Wyre's "tools" in many cases are gimmicks that are based on very specific behaviors from Oblivion that don't always hold true even in closely related games like FO3/NV. It's still an excellent tool for some users that are already familiar with it and who have enough knowledge to work safely for it, but it's like giving a nuclear option to new users. Most of what it seems to do automatically aren't safe without some manual intervention.
You mention the "only" thing MO2 offers being virtualization. There's no "only" in that. That's what allows both MO2 and even Vortex to be essentially *completely safe* for either newer users or those who don't want to build the knowledge base to use the tools safely.
There's another user on here, a long time mod author, who will state that his preferred method is to manually install everything, and validate all changes through the GECK. That works for him because he has literal decades of experience doing what he does in his way. Would you recommend that method to new users? Probably not, and for the same reason that I wouldn't recommend more arcane and more generally "unsafe" tools like Wyre that encourage users to do things that, more often than not, will do more harm than good.
Bashed patches are not a cure-all, and nor are they a sensible thing to do unless you actually already have the knowledge to do it manually anyway. Recommending them to someone who is having to ask a very basic questions about LOD is not a responsible thing to do.