I guess that isn't any worst than taking a fist full of E7018 electrodes and knocking the flux off of them and using them to slug the joint.
So is the flat bar too short (12mm too short)? What purpose is the rod bar serving other than saving a few passes of welding?
If the root opening is too large, the proper way is to butter each side of the joint to get the root opening corrected and let it completely cool off, then weld the joint as normal. (AWS D1.1:2010 Clause 5.22.4.3) or (AWS D1.1:2010 Clause 5.22.4.4)- getting the EOR's approval