Ok, I found it. I'm pretty proud of myself, not because I was able to compile by myself (because I couldn't! 

), but because I searched for an entire day the quickest solution.
A little tutorial is a must. If you need q3map2 64bit you have to:
1) Go 
here and download GtkRadiant-1.6.4-20131213.zip. Unzip it wherever you want and copy the x64 in your netradiant folder so your netradiant folder structure will be
netradiant-blabla-win32
 --x64
 --games
 --gl
 --and so on
2)go in to the game folder that you need to modify (for example Xonotic.game) and edit default_build_menu.xml with a text editor
3) change [RadiantPath] with C:\yourprogramfolderpath\netradiant-blabla-win32\x64\q3map2.[ExecutableType]" and save
4) Now open your map and add this key to worldspawn entity:
key: _blocksize (don't forget _ at start!)
value: 32768 (or bigger, as long as power of 2)
5) compile and you're done!
In 2 minutes (but without lights), I compiled without errors a map 91360x76848 units!I took four minutes to go from one side to another! 

With q3map2 it was crashing at FloodEntities point with
ERROR: LoadPortals: couldn't read prt, etc.
Now it works!
EDIT: scaled the map to NetRadiant maximum grid bounds (130000x130000) and player walks for 6 minutes and 50 sec before reaches the other wall!

There's a way to increase NetRadiant grid bounds?