When using Alien Biomes, the decoration reduction gets applied only to the vanilla biomes. However, the removal of fake rocks does work on both the vanilla and the modded biomes.

What do you mean, exactly? I just ran a (very cursory) test and at least from what I could see at the first glance it seems to be working fine. Are you using only Alien Biomes, or is there also something else that changes decoratives or map generation?

Please take my comment with a grain of salt. I was trying out Space Exploration (Alien Biomes is obligatory for it) and I had the settings of UnPollock set to 0.25, however, from my eye at that moment, it didn't look like there was any less clutter on the ground of Alien Biomes. I did not conduct any further testings as I should've before posting anything. I'm not using Space Exploration anymore, nor Alien Biomes, since it keeps adding purple and yellow flowers to the floor that I really detest, with no option for removal...

Important to note that if SE is installed, the config options of Alien Biomes are modified, therefore IF my claims of incompatibility are true, it might be related to SE rather than with just AB.