Hello J
The information seems confusing......initially there are cracks findings......then the MT/CWI literally told you on a FCAW job originally to weld all the toes of the welds with GTAW and then feather them in with a flapper wheel. Huh!, toe cracks to be covered by GTAW welds:


? Then you should reply by saying " D1.1 states..."repair of cracks needs prior approval of the engineer".
You have higher chance of winning your case, you call the Engineer in charge to come down and show to him with the help of your old friend that the crack finding given by MT/CWI is wrong.
No Engineer's instruction, means no repair on cracks. Otherwise, you are violating the code requirements.