How is calculated fill-factor percentage related to size of database?
What you see is correct.

When you rebuild an index first the new index is built and only then the old index is dropped. And if you don't use 

SORT_IN_TEMPDB = ON


the space that server needs to make a sort is allocated within your db

Your db has now empty space, it's not space reserved to any object, it's just free space
(space that was freed after temp objects needed to do sort were dropped) 

So your indexes are not empty on 42%, it's your db that is empty on 42% and if you do ashrink of data file (I don't recommend it) your db will occupy only 82Gb