1 & 3: I'll look into these.
2: Without using ridiculous amounts of either memory or processing time (especially on larger levels), there's a limit to how much this kind of allowance for overlapping objects can happen. The priority isn't exactly "radiation has priority over splatpad" as such; it's just whichever object is last in the object order has priority. To fix this with anything resembling the current way of working would need as much memory as 64KB per pixel, or around 3GB for just a single screen. I have one idea of how it could be improved somewhat, although this would still only allow overlapping of object types that the individual object does not need to be tracked (only the type does) plus one object per pixel where it does, so for example, you could overlap a triggered trap, a fire object and radiation, but not a triggered trap and a pickup skill (as both of these need to track the individual object).
Of course, eventually, the ideal approach would be to allow for overlapping of any number of objects, but I'm not entirely sure how best to achieve this.
EDIT: Re: point 1, in terms of that they fall down and turn around, this is intended (it will even happen *two* pixels from the edge, and will also happen with walkers). However, there are other issues here that should be fixed, see attached level.