I've heard that the small squares are used to try and prevent water migration throughout the entire core. They are usually oriented so with the grain at 90 degrees to the adjoining pieces to limit the pathways for water to travel.
I found the same thing in my Sailfish tank covers. Pulled them all out and replaced with 1/2" ply.
At the start of the project, the bottom glass was cut to allow for easier removal.
Core squares removed...
Grinding completed in preparation for new core...
Prior to laying down the 1/2 ply, I drilled a bunch of 1/4" holes in it that would allow resin to escape as the ply was pressed down. Then I painted a coat of unthickened epoxy on both the panel and the 1/2" ply. Next I put down some epoxy thickened w/ wood flour using a notched trowel and laid the ply in place. It was weighted down with a bunch of cinder blocks.
Once that cured, I glassed the top. As you can see the new core was cut so it stopped about 1-1/2" short of the edges of the panel and the core edges were beveled at 45 degrees to allow the glass to wrap easier.
I started with a strip of 1708 in the channel around the edges. Then a layer of 1708 over the whole thing. Then another strip of 1708 in the channel. Lastly, a second layer of 1708 over the whole thing.
What this did was isolate the core from the screw holes around the edges. So, even if the 5200 I bedded the screws in leaks, water will never get to the hatch core.
Hope this helps.