It does not create a Fallout ini. I don't know where you are getting your information from, but it is erroneous. Saveini can cause issues, but that doesn't necessarily mean that it will. My issue stemmed (i think) from using the old ini from pre update...can't speak for op though.
Here's the deal for me; after a complete reinstall of Skyrim (same save game) and using the saveini command again, I took a trip back through one of the offending dungeons. I can happily report that I maintained a steady 66 fps (my monitors (forced) refresh rate) the whole way through.
@OP: It may be a bit drastic, but maybe if you did a complete reinstall of Skyrim that might help. If you use the saveini command, then just be careful of which settings you alter.
A simple search of the forum:
It's unwise to use an ini created by "saveini". There's a bunch of settings in there that, when loaded by Skyrim, cause undesired results, despite being spit out by the "saveini" command.
Just typing the command "saveini" causes instability, makes your loadscreens red and breaks the map. To fix this on the PC you have to delete the generated INI file. You can't do that on a console, so you'll have a broken game.
SAVEINI will dump Fallout's old INI, not Skyrims INI.
SAVEINI is not a Skyrim command. The INI it creates is NOT compatible with the game. It has options and functions that are no longer used, and some crash or cause other issues, with the listed values. Specifically related to physics, and effects with LOD levels. It even says "FALLOUT" as one of the folder locations. That should have been every-one's clue that it was not an INI for this game. This is NOT the fallout engine, it is a creation made from that engine. It is the Skyrim engine. LOL. (Still Oblivion.)
Everyone rushed out with hacks, and attempted to look like they knew what they were talking about, and to be the first to publish this stuff... Without actually testing anything, or knowing what it was actually doing.
(Not all, but many. Anyone who ever instructed you to type SAVEINI, and use that file...)
As far as the .ini being non-adapt I was having some doubts myself as I noticed the file had values such as "one limb didìsmemberment" an "reflect explosions" for water. there was even a variable with the word "bullet" in it.
I also noticed the Fallout line, now I know why!
There are a lot of obscure and apparently usused settings that show up when the 'saveini' console command is used, like this little enticing nugget:
Yeah there is a bug using saveini in the console. It places the ini info in mod ini's rather than the "My Games\Skyrim" location. The ini I now edit for all in game settings is called 'dD- Realistic Ragdoll Force.INI' in the Data folder.
The INI it "dumps" is the INI from fallout, which is not used in the game itself, but it is contained in the games source-code, so that is what is dumped. The "SAVEINI" command is NOT a skyrim command. it is a fallout command, thus, dumping fallout data.
But I don't know if its relevent to the OP as he says he hasn't delved to deep into the .ini
But before making .ini changes I would advise trying windows mode and Medium quality preset. If it works, increase settings gradually from there.