Currently I can play w/o problems so this is just a reference point for others and maybe for someone keener than I to deduce the root cause.
Also, this might be a problem on MO's end, but since I have a second problem while not using MO, I figured I'd start here.
Everything's installed correctly (ENB + preset in actual skyrim folder with the suggested modified .ini values)

ENB alone: objects behind trees show through (w/ suggested .ini value changes)
ENB + MO: Missing Textures (w/ suggested .ini value changes)

Details:
Originally, I had problems with a bunch of missing textures at the start of the game in Helgen keep (screenshots available) using MO launcher and ENB. I disabled every single mod and their .esp through MO and that didn't fix it, so I assumed there was something wrong with my real Skyrim data folder and started with reinstalling just the game.

Using skyrim launcher (not MO) the textures were fixed. As soon as I reinstalled ENB + presets and modified the skyrimprefs.ini file in my skyrim folder accordingly, (triple checked every value) I started getting a problem I'd seen before with incorrect MO .ini settings (objects behind trees showing through, I believe the bTreesReceiveShadows value was responsible, SS available).

>The part where things get confusing<
Launching through MO with ENB and 0 mods activated showed no difference from before I reinstalled skyrim; missing textures, but the trees were shadowed correctly. So I tried literally swapping .ini files (copy+paste) from MO's version (w/ suggested ENB .ini changes) replacing my base skyrim .ini, so I'd know the values were 110% correct and that should fix my tree issues. It didn't, objects were still showing through trees, and my textures were still fine.
Swapping from the base skyrim .ini (w/ suggested ENB .ini changes) replacing my MO .ini fixed everything.

So, it's got to be a problem with my .ini files or the way they're handled. Although, if you couldn't make sense of all that, the confusing part is at the end of my troubleshooting where both my base SkyrimPrefs.ini and Mod Organizer's skyrimprefs.ini files were exactly the same (copy+pasted) and I'm [still] getting two different gameplay results. w/o MO launch = objects showing through trees) I have copies of all the aforementioned .ini files if anyone wants to peruse them.

Objects (mtn ridge) showing through trees with some weird DOF behavior.