Hello there!
So right now I'm writing a story, which - for the purposes of style and plot - I'll divide into 6 parts. Now, the general tone of my story gives it a solid T rating. However, there will also be some NSWF elements that naturally elevate the rating to M. The thing is, not every part will include those, and I don't want different parts of the story to have different ratings. Imagine reading half of the story just to suddenly learn that the rest of it is inappropriate to your age and you can't read further - I myself would be very frustrated. The only two ways I can think of to pull this off is to set all parts to M rating, which likely will be against guidelines and just doesn't make sense, or to include in the main story only "censored" T-appropriate versions of the moments in question and create a separate story that will be M-rated and will contain all moments as they were meant to be. The second option seems good, but most of the NSWF moments will still be essential to understand character's thoughts and growth, and I'm a little scared that I won't be able to fully translate my ideas to SWF version. So, what is the best solution to my problem?
Thanks in advance!

7905307
Make a spin-off. Hint at the nfsw stuff in the main story and then write a spin-off for the people that want to see it. Unless it if important to the story. If that is the case, you need to change itbecause it's not worth it changing the story age rating, or changing your vision half-way.

7905307 I've come across this issue multiple times. I've used the following 3 solutions:
a) Avoid NSFW details. Write everything in E rating.
b) Embrace maturity. Slap on M rating. You don't need to do that right away though; you can do it when the story starts going into the NSFW territory.
c) Publish a different story that features NSFW elements, but make sure that each story can stand on its own.

It will not against guidelines... if you rate it M then you are promising that part of your story is worthy of M. M stories can definitely have T or E content. It takes Cupcake level gore/M stuff to be that and few can make a good story like that.

Keep track of which characters are engaging in M behavior and which do not. (Since you will likely use character tags I assume you know roughly how often a specific character will appear) If there is a clear difference then an entire side story can happen with the cast of both making regular cameos or even supporting roles.

Even something as simple as;
Rainbow Dash

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Thanks everyone! Thankfully, the moment when I plan to introduce NSFW elements into my story isn't nowhere near, so I have plaenty fo time to reach some decision. Your advice was very helpful!

7905743
One other thing I forgot. Use the author's note to advertise the spin-off, if that is what you'll do.

Try to keep such notes at the bottom. A great many readers will not read or be otherwise disgruntled when the story they chose to read has two sets of tags. Which is why it is important to have both be able to stand on their own. It still won't stop people from leaving but more will stay if you hook them good on the first chapter with a NSFW story disclaimer at the bottom.

To pick on poor Pinkie

The first story is a nice friendly story of Pinkie Pie trying to befriend a series of the most prickly ponies you think up. She wins some, she loses others (who mysteriously vanish afterwards) and everypony (but Pinkie) learns the valuable lesson that you don't need to be friendly friends to be a good and decent neighbor. The final chapter(s) will suddenly have Pinkie Pie in an asylum getting the help she needs. While it will come out of left field to those who refuse to read the other story they can be comforted to know that she survived.

The other story is... Cupcakes ... Let us not pretend you didn't see this coming. I'm going to keep going on this hypothetical story as that will give a decent foundation for such a story if anyone steals it (be my guest). Starring in this M rated fic will be Pinkie Pie and Twilight (serving as our Holmes) with each chapter dedicated to one as Pinkie kills and Twilight keeps Rarity (who wants to be our Holmes and starts out as our driving force for Twilight's side of things) alive and out of jail. Starts out as a mystery before adding the murder to the front of that half way through. Play up the horror here of the first (found) homicide in Equestria in years/decades. Perhaps it is the first one Rarity has ever heard of due to cover ups and Twilight/Celestia informs her of the sad fact of life; ponies can kill.