This is purely a guess, but the engineer might feel that the existing welds alone won't be sufficient. Plug welds may or may not be as strong as the bolts, it depends what bolts were used and what You plug weld with. OR it might be a CYA, open holes look like something is wrong, plug welds don't. In the end it is the engineer who signs off on the job, so it is His call.
I agree with you in that open holes attract attention and make people ask: "What is not there that should be?". Generally speaking, leaving the holes as is probably would cause no harm, especially where it was mentioned that siding is attached with them, but it is the engineer's call.
Dave the bolt hole goes through a 4X4X1/4 HSS which is split down the centre to slide over 3/4 inch plate 14inches which is then welded solid both sides of the plate. There is only one bolt hole which was used for erection purpouses ?????