I think the issue with picking alternate colors for a level palette is that they have to look like they're "in the scene."
So in these examples, since ~98% of the room has a brown cast to its coloring, you'd want any additional colors to reflect the room setting by also having a brown cast. The original green sort of leaned in that direction, particularly with the brown-ish highlight, but the newer green with the increased red values really leans in that direction, and makes the borders look like part of a cohesive whole.
On the other hand, the blue coloring doesn't look like it's being affected by the room lighting at all. Rather, it sticks out like a post-production overlay - you know, like those "obvious" Photoshop jobs or CGI effects where even an amateur can see that something's off because the editor didn't fully bring the new element into the existing scene (almost always a lighting inconsistency).
Of course, this is a bit of an odd discussion to have in this particular context, since it's not as if sprites are changing color casts to reflect their settings. Still, having internal consistency in each level palette is at least a step in the right direction toward overall color coordination.