Leaving them out entirely, like IDW did for the individual volumes, left SERIOUS plot holes. Like, MASSIVE ones. Especially when one of them had nothing "controversial by today's standards" in it, and NOT omitting it would've at least filled in probably one of the biggest plot holes. (See how I fixed it for myself
here.)
Because nothing in them (waitforit) is truly offensive, and mostly just educational (like you said, a history lesson), if not typical TMNT silliness, the only thing that would probably need to get edited at all, let alone out, is Chris Allan's drawing of the Prophet Muhammad (there it is

). I can't see them reprinting that in any way, shape, or form, which is dumb (especially when South Park treated it way "worse" a decade later, and even got away with it for two whole episodes before anyone caused any stink, and when bringing it up, everyone
still always forgets those first two episodes where he was completely uncensored).
Luckily, my volume 8.5 has it untouched. Of course, that won't help my fucking autistic OCD, having to go to another book in the middle of a book (the compendiums), whether they only erase that one image or leave out the issues again.
#32 - The Good, The Bad, and The Tattooed - Tattoo has yellow skin, like his original action figure. Which I don't see as "problematic," because literally not a single other Asian character in the entire series, let alone THAT EXACT ISSUE does. In fact, before reading that issue, when his figure came out, comparing him to Shredder or Hamato Yoshi, I always assumed his yellow skin was a mutation, and not harmful race-coding. But I'm white, I don't get to make that decision. Alls I know is I desperately want NECA to make an Archie figure of him, yellow skin & all.
#33-34 - The Karma of Katmandu & The Search for the Charlie Llama - Welp, if IDW is as worried about losing China sales as Disney is, that's why they won't include these two. Even though Charlie is a legitimate Llama. But he IS still handled like the Dalai Lama regardless. And they're all in Tibet. Which, I don't understand why Trump & the MAGAts hate China so much - they're a racist dictatorship, we're becoming a racist dictatorship...
#35-36 - The Black Stone & Steel Breeze - This not only fulfills a dangling plot thread from earlier in the series, but then opens up a new one for later, especially the "semi-official/mostly fan-made" ending to the series. But yeah, the story of Islam, Muhammad, the Quran. 35 has the very respectful-looking singular bust drawing of Muhammad. Muslims don't want his visage portrayed, meanwhile Christians are putting Jesus' corpse up on the device he was executed on...I've been wondering lately, what if he'd been hung? Would there be little gold nooses on chains around people's neck? Wooden nooses hung up on a nail on their living room walls? (No disrespect to any Christians here, but I was raised Evangelical, and I lost my faith for lesser hypocrisies than what is currently being displayed by "Christian" Conservative Nationalists, so I am vehemently NOT a fan of those fucking pieces of shit. But yes, #NotRealChristians.)
The biggest offender for omission, for having literally not a single "offensive" thing in it, by
anyone's standards:
#37 - Stump'd Again!! Including it would have a minor plothole as to where Cudley picked everyone up from, as he picks them up in the desert at the end of Steel Breeze (#36), but not as big of one as leaving this issue out. It's also the ONLY appearance of
El Mysterio, whom we're getting a figure of imminently. And it not only leaves a plothole for issue #38, but I believe a few more for later in the series, as well as the Mutanimals spinoff.