Awesome! Thanx for your detailed comment.
Actually we don't want any solar gain in this climate. There is a northern window to let the daylight in, but the idea is to keep direct sun out.
The skylight is mainly for air flow, and we have three cooling tubes installed already (not shown on the plans because... just because) with a decent incline. The may have to be extended though, as the berm is likely to grow thick behind the 3.5 meter wall.
Hahaha, for the opening of the skylight we have thought up this neat lever that would push a little palapa structure up through the hole, with a palm-thatched roof and no walls. However, for this year we'll probably just seal it with a tarp and do the fine work next year.
Thanks for your suggestions regarding the opening. I know that box of rocks you mentioned and agree: there have to be better options.