Still if there are shards of plastic loose in the case have it reholdered while it is free.
I too have an oddly situated book in a slab, TMNT #4 2nd print: regular slab but with tabs the book is not centered but adjusted to the right side of the slab.
There was at least one other slabbed this way that I was able to find online at the time. For whatever reason I'll trust there was one, a reason.
No loose shards so I didn't reholder, but something I'll admit made me question why?
Mag holders are a different breed as cumbersome and large, that too I'd struggle to over come for a reason, as you said and even my TMNT most others were encapsulated "normally."
Take all with a grain of salt and do what your gut says, but at least get rid of the plastic loose shards with a reholder while the night is young.