Yes, it can be done.
The process is:
in a 3D editor of choice, make the new pitbox cubes and the new start cubes, oriented with
Y axis = top/bottom direction
X axis = left/right direction
Z axis = front/back direction.
Call the model something like new_pits.kn5
Add the new .kn5 to the models.ini file, in which you list the .kn5 files to be loaded in the track.
Done.
I would like to leave this version of Misano as it is, but you can do the modification and share it in your league or group of friends.