I'm no engineer, but I seriously doubt that weld metal in bolt holes will replace bolt values, especially for the stresses that these columns are going to be subjected to. I have never heard of this as a method of correction. I would definitely stress the degree of difficulty to the EOR. If the EOR approved plug welds, keep a copy of the documented approval, which should be signed by the EOR. Also, document your concerns, referencing specific D1.1 plug weld limitations and specific AISC design criteria, and make sure you've addressed your concerns with regard to the difficulty in acheiving the required welds. If you can, email it to the supt. and/or the EOR, and ask for a delivery confirmation. This documentation will be critical down the road, should a failure occur.