Yep, the GBA Expansion sticks out a but, and the card isn't flush to the top of the DS. And you do need a bit of force to push it in, compared to an R4 at least.

 

i would use 2 fingers to push the ds cart in. don't use your nails. the plastic is pretty soft and over time you're gonna put an indentation in it. as for the memory card it seems fine on mine. you should use your nail for this. btw, when you try sakura can you let me know if on boot up you get a message on the bottom screen about how it can't check your disk?

 

Well i was pushing to the point where i had to push the M3R right to the end of the slot before i could feel or hear a click, the R4/Dstt i've had never did this (as in i never had to push the cart right to the end of the slot)

The memory card is a similar situation. If i'm pushing to eject it out, sometimes it feels like the spring is going to make the sd card get caught inside the shell...

 

I have no problems you mentioned in your original post, my expansions fit flush in both of my NDSs, and that problem with big chip under the label, so it needs a bit force to put it in, is solved with new board design..
I have absolutely no complaints about M3 Real now..Sakura fixed everything I was bugged with..
I have first batches Perfect bundle..