For Defect #1
What you describe for the first defect sounds to me like the melt-thru on the back of an aluminum butt weld. Sometimes you can see a little line where the faying surfaces came together. Sometimes with poor surface prep or improper technique that line can become an inverted depression.
If you judge that discontinuity to be a lack of fusion (which it sounds like to me) it cannot be ignored.
1. You would be in compliance to reject it outright for failing visual per table 6.1 whether or not it the defect is in the base metal or out of the measured base metal thickness in the reinforcement.
2. you might consider an adaptation to your WPS to encompass rework, but this is a sticky wicket because technically rework occurs after inspection, not before (5.19) or you could try to stretch the meaning of (5.15) post weld cleaning, to cover the removal of excess melt thru, that when removed renders the coupon acceptable.
I don't like either alternative. The discontinuity you describe says there is something wrong that you would certainly not leave on a production piece eh?
Why not have them try again with better focus on surface prep and torch angle, including the root faces, no matter how thin the material. Shears out of adjustment or used for multiple purposes are known to leave ragged edges or gunk on root faces, and just a few swipes with a new file can make a huge difference on melt thru profiles.
For Defect #2...... A piece of filler rod still fused to the test coupon? is that what I'm reading?
I guess you have to decide if you are going to visually inspect the whole weld or just the poriton that is to be sectioned... If it were not lack of fusion or a rod end, but a crater crack, would you accept it just because it was at the end of the coupon and not going to be sectioned?
So my opinion...... If they were production welds I would send them back for repair... But since they are performance qualification welds I would reject and retest for the reasons above.
Al has done a lot more testing than I have.. Would like to see his opinion.