Xaviien

Ignore the warning.
 
The option to switch off the warning is described on the MO mod page:

You are correct. Obviously you can't install options that require DLCs you don't have.
STEP now only fully supports Skyrim Legendary, ie all DLCs. You can still use the guide, but you'll obviously need to be careful when installing some mods.
 
If you notice any that mention downloading a certain version of a mod if you have all DLC, or a different version if you don't, please feel free to post links etc here, as it will help clean up and remove those type of instructions to make things more consistent.
Thanks.

That would be annoying, to say the least, if downloading the SRO torrent which is over a gig.
Also it seems to be limited to normal browsing, at least here, so you may not even be able to do it.

1. VERY limited support will be provided if you are using NMM. The guide assumes you are using MO.
 
2. Let's just say mod A provides 150 files, and mod B provides 50 of the same files, only better. You install mod B after mod A, so those 50 files are provided by mod B, and the other 100 are provided by mod A. Mod B overwrites mod A, where necessary.
 
3. High Quality 3D Map and A Quality World Map provide different parts of the map, to give the effect desired in STEP.
Once you have them both installed you could check which files are provided/overwritten by each mod using MO. Not sure if you can check that in NMM as I have never used it, and I likely never will.

https://wiki.step-project.com/Guide:Mod_Organizer#Troubleshooting
 
I'll just leave this here for you...

From the STEP Mandate:
This is the best reason I can find for the baseline being fairly "middle of the road".Most of the mods give Skyrim a major facelift without degrading performance. Depending on your system you can easily get away with all the higher res options.
 
You can also see the discussion thread for almost all the mods by clicking the W icon after the mod name, which will open the wiki page, then clicking the "forum" link near the top.
Be warned, some of those threads are quite long, and don't always explain exactly why certain options are recommended.

1. Having MO etc outside the Skyrim directory just means you need to tell them you are trying to play/edit Skyrim I believe. Having them in the skyrim directory allows them to pick that up automagically.
2. Use the ini editor. To access all the options in the configurator you need to change from "basic" to "advanced" but you still can't delete items. I think. Definitely easier to just copy the new lines into the ini using the editor though.
Be very careful not to duplicate anything, and the only spelling mistake should be in the word texure.
3. You are correct. MO makes a new ini for each profile, and your original skyrim directory remains untouched.
 
The definitive answers to all your questions are actually all in the guide/s. Make sure to read carefully, and some instructions are on the "Detailed Instructions" pages.

Based on what I read in a thread by an author that is making some kind of megamod, having Sounds of Skyrim and Audio Overhaul Skyrim causes a lot of sounds to play at once. I don't know if that is unique to his project due to merging mods together, or if you might run into a similar issue. You do seem to have quite a few mods doing very similar things.
Have you looked into any of the other mod guides, like GEMS? Or even the STEP Packs? Plenty of people have looked at a lot of mods and figured out which ones do what best, and which mods conflict with each other.
When I first got Skyrim and looked into mods, GEMS caught my attention, but the first step in that guide is to install STEP, and I kinda got waylaid here hahaha
Yes. If you follow the STEP guide, they should be in the order you mentioned.
Basically, once it starts listing the mods, from section 2.C. Extenders, everything should be in the order listed in the STEP guide.

There may be some variance in mine, as I got tricked by the scary MO warning about mod order:
Once I realised we are meant to ignore that very clear warning, I had to go back and manually reorder my mods. Luckily I had taken a screenshot of the warning to post a bug report, so I could use that to figure out which mods had been moved. Fairly sure I got them all back to where they should be though.