If I understand you correctly the water line comes up
directly behind the toilet???
just shorten the nipple comming out of the wall
then install a new stop or put an elbow on it
whichever works out the best.....and then get yourself a
16 inch flexible braided stainless steel supply line
and install it... and just forget about it.
sometimes looks under a toilet arent worth the time
or trouble to make look all that pretty.