It just takes some time to know what you are doing. Like pure graphical mods (textures) are usually OK to install without any hitches. Script heavy mods? Thread carefully and see if it utilizes SKSE and so on. Read the comments, read the manual and stop and take a pause if you are just guessing at things.
If you stick to those rules you should be OK. The problem is that in order to learn this you need to mess up a couple of times.
What I do
0) Have vanilla skyrim
1) Save right after the start when you are in the village
2) Slowly add mods, start with basic textures and models.
3) Check if everything ok, play for half an hour, e.g. go to Whiterun.
4) Save your mod profile every now and then.
5) Add the difficult mods that tweak and change things and are script heavy.
6) If you mess up, you always have your vanilla save and probably the profile that worked for you. With steam verify local cache.
Thats what works for me.
This is what everyone should be doing. In fact, it is not hard to create a Vanilla save even we didn't create one in the past. We can recreate the Vanilla Data folder. The easiest way is to rename Data to Data1 (or anything). Ask Steam to check file integrity, in which it will redownload Data folder for you. Or you can just manually re-create Data folder by copying all Vanilla files over (given you know which one they are). And with MO2, you can simply run the game outside MO2. ENB doesn't bother your save because no data from ENB will be written in your save. Skyrim doesn't even know your ENB exists.
But having a save at Helgen doesn't mean a whole lot. Game progression comes with many stages, imagine you are at level 80, if you lose that save, and have to go back to Helgen level 1, how would you feel? Recreating your level 80 with console command is possible, but not fun. Replacing all those items you didn't yet earn feels like you are losing the personal touch. For example: I don't particularly like the Dawnbreaker. But one day I did the quest and got rewarded that weapon, nice surprise! (Because I totally forgot which quest gave Dawnbreaker). So Dawnbreaker means something for my character and myself: that late night I was trying to finish the quest and I kept dying, or someone kept messing something up, or something painful I had to go through (both game and RL) to earn that thing.
Again, not going against everything you said above, but all these are not even enough. Here are a few things I ran into that was rather game breaking:
- Looping OSA script, papyrus bloated to 2Gb log file, so glad someone found a fix, I didn't have to go back to old save.
- I use Quick Light, and one day the lantern stopped emitting light. It's not a Load Order thing, because old save worked. I tried cleaning with ReSave, uninstall and reinstall Quicklight, no avail. I went back 2 days of progress, would have to redo 3-4 dungeons (have yet to do).
- fxRandomDust script ... someone found a fix, thank god no going back to old save.
- Better Vampires glitched out, I found a fix. So glad author changed it after I reported. But I had to go back 1-2 days of progress because I don't trust a glitched out vampire.
- XPMSSE glitched out, something to do with weapon scaling script ... random CTD + CTD on save. I followed a fix, not sure if it is fixed.
- Game still CTD on save yesterday. I couldn't find a reason, going back to old save (5 hours lost) .... it is quite stable ....
All of these are problems that don't immediately pop up in my face. So certain mods feel deceptively perfect ... will cause troubles that I will find much later on. OSA has this eye looping script that causes log file to bloat to some 2Gb-3Gb (imagine a text file at 3Gb, that is like the amount of text US library of Congress combined). The only thing is to keep saving a lot with a long list of save files. Each file is around 5-8Mb, at this day and age, can be nothing. But still, the worst thing can happen is random CTD. Because things like black face I can live on. Some of my vampires still have black faces, but since I barely meet them, I don't care anymore.