My entirely uneducated guess is that a layer of paint would impede the cooling of electronics that depend on the housing to dissipate heat.Paint would also absorb more solar heat than plain metal.
A dye bomb is used for aerial crash/rescue. That would contaminate a surface, but also provide a possible visual marker. Maybe several launched away from the lander, but which could be used to triangulate it, in the rare case that might actually be of interest.
I suspect there's a lot of re-thinking of how to land on a comet going on as well.
Certainly I started thinking about better ways once this image made it clear what we (humans) are dealing with here.
I can imagine a cage-like outer shell where the robot inside is able to rotate on two axes under power. Let it tumble any which way and then use sensors to determine the correct orientation and right itself.
That's pretty much what Spirit and Opportunity's airbag landing system was, although a lot simpler --- it was set up so that no matter what way up it was after it came to a rest (after bouncing and rolling!), when the bags deflated it would automatically roll the right way up so that when the deployment mechanism finally opened, the rover could just drive out.
I've tried to find a video showing it happening, but while there's lots of animations of bouncing, rolling, and the final opening up, they all miss the critical moment. Also, car safety videos are really badly poisoning the search results...