Basicly, you have a couple options there... You could run your area a couple times, once with your pine forest in the snow, and once without the pine forest in ght snow. then clear the areas out by melting areas, and removing trees, etc.. bla bla bla.. yes, that is a lot of work.
two, you can use a second dragon setup, (I recomend this so you can revert back to the default Dragon scripts easily) and modify and edit your Groups, and mapTrans.txt files.
I did this same thing you talk about as matter of fact.. made 2 colors, one was the regular snow tile, default on Mod9 pallete, that i removed all the trees from, and another i took from I believe, cobblestone colors, and made them snow tiles. (in the mapTrans.txt) then in Items folder I simply copied the Alpine.txt, name it Alpine2.txt, edit any trees you want in there, and set the group in Items.txt to the once cobblestone color group, that is now Snow to place the items in Alpine2.txt
Complicated? probly sounds complicated, but with some trial and error, you will get the hang of this, and find it is very efective
I might have lost myself in that description.. so if you got confused, I will try to re-explain it.. *scratches head*.. too many things i am trying to do atm..