OK, here is what I did meanwhile:
get the newest blender files, which shows the following: There is the mentioned aluminium plate (think of it like a stencil), which has the Logo craved throught. This fits into a rectengular pocket of the lid.
In the bottom of this pocket is an elliptic hole, which holds the clear acrylic part, which has the Logo embossed on top to fit into the aluminium craving. this part distributes the light from the RGB LEDs which edge lid the plastic part.
These 2 parts are glued int the lid. Every modification in the mold would result in making the lid smaller, which in reverse means to ADD material to the mold, which is the most costly thing you can do to a mold, so no chance here, I'd say.
BUT, I also talked to hns and gave him a sketch of my idea, which is like this (given, we have the 2 logo parts removed already. I get to that part later):
There is space to drill 4 holes into the corner parts of the logo pocket (besides the elliptic hole), so in theory there could be a hack to make a "screw from behind" (pun intended) logo. So from the communication with hns I got confirmation, that there will be room for the heads of the possible screws between the lid and the LCD (PCB).
So one option could be to make the Pyra default setup to get it with the logo not in place, but as a kit. Like you get the Pyra with the hole in the lids and decite yourself to weather glue in the original logo parts or to make your own. Or maybe it is even easy enough to remove, that that would not be necessary.
OR
@EvilDragon : How much complitacted would it be to e.g. give the pre-preorderers an extra lid-part.
I'll try to get hold of some lids (perhaps production fails) to make tests and examples as soon as it#s possible