So, all happily resolved to my satisfaction both with the dealer and with Honda, both of whom I have to say have been remarkably responsive and helpful.
Just on the stitching issue. As was noted by a couple of other posters this is now the standard manufacturing process on mk2 T38s however unsightly it is - you can't actually see it when the boat is inflated - but it is on all new Honwave boats (and many other brands) with inflatable floors AFAIK.
I was also interested to note that many of the structural joins are actually stitched, and glued as the construction of the boat is a fabric material impregnated with plastic (PVC)
- I thought they were just glued.
Also and have the below from Honda:
Factory have now confirmed that the stitching holes in the floor to tube seam tapes are completely normal and part of the assembly process. The tape is folded in half along it's length and then machine stitched along the length about 15mm in from the fold. The whole tape is then glued to the floor sections and tubes in a pre-folded condition, for ease of assembly. Once the glue has set the stitching is cut from between the folded sides and thereby released to take the shape of the assembled parts.
This does leave the stitch holes somewhat visible, especially when the boat is deflated, but does not affect the structure in anyway. This is standard assembly method and we have checked around with other dealers to confirm they have similar assembly evidence, and they do.
I feel somewhat more knowledgeable about SIB construction and will be ready for the water in a week... just in time for it to get really cold!