Just follow the guide for the Outer Case Replacement to take out the power supply and the cage, then you can safely remove the HDD and replace properly.

On my model, the motherboard is held in place with another six (i think) screws which go in the steel posts that support the motherboard. This step is completely missing in this guide. Interestingly enough, in the bottom panel removal step, the photograph does not show the screws, as if somebody had removed them: i honestly don't think that in any revision Sonos would leave the motherboard secured only by the screws on the back, where the connectors are, because the motherboard would rattle with music.

Are you referring to the 10 pin connector in Step "Motherboard"?

On my model, only 6 of the 8 screws hold the bottom panel. Looking at the picture above, where the screws are circles, the bottom row of 5 screws, the second and fourth screw are threaded for nuts, as opposed to the other six, which are threaded for plastics. These two screws can be removed once the bottom panel has been removed.

I pulled them out using the corkscrew method: I drove a screw about 10mm deep into the rubber plug, then pulled up the screw. This method created way less damage than other methods i have tried.

NB: in the photograph, two antennas of the three soldered on the antenna PCBs are broken: You can see one standing upside down towards the center-right of the photograph