Hmm, later I'll try out changing the unused (in Mukamok they had the same color as the background color which shows transparent in the maps) colors into different ones, and we'll see, if they'll be still remain transparent, or it will do something with the background...
EDIT: I've found some interesting things. In the last row of main palette there's a color which one is always the same as the non used last color in the BGtileset's palette. In Mukamok's palette there was a yellow color which is pulsing in the levels, if I draw with it on the tileset. I mean changing color from brighter to darkar, than back. And there was a 3rd color, and when I used it it made samething similar when you make a JJ2 level without background. Strange. I wonder what are they for...