The house clearly has a defect and does not conform to the standards it should have been built to. That's not debatable.
Whether it may or may not be OK, is debatable. But no qualified professional person is going to certify that and support any assertion that the mortar is acceptable now or won't deteriorate in the very near future (when the Buildmark warranty expires). So there's a massive risk.
The OP is in a corner with limited options.
If he is minded, he could put the house back on the market, come up with some plausible reason for needing to sell, pretend no knowledge of the condition and take a hit on the sale costs and be free of the problem. But if things come to light at some future time, then there is that risk of being sued, and the OP will have to shoulder that risk for six years.
Otherwise, the other option is to accept the repointing offer and hope that is successful. The offer would likely be full and final, with no chance of further claims if unsuccessful. Again, a massive risk, and I wonder if any independent person would certify that. There still comes the risk at sale time and a clued up buyer's surveyor could cause problems for the OP - no sale or significant price reduction.
So that leaves legal action. This would almost certainly be successful and most likely settled before court so would not be protracted. There may be initial costs and stress, but costs would be recovered and stress compensated. And there is a certificate declaring that the house is satisfactory and not defective, so at sale time there is no problem.
Linked to this is whether the OP wants to live in a house with the level of work required having been done, or would rather have the house bought back by the builder and costs paid, then find another house somewhere else.