I've never used the Dingotone stuff (and never will as it's Australia-only) but I belive the intensifier coat should help deepen the colour.

As you couldn't see it but it didn't take stain well, the mark could have been a glue smear. You normally only get them on veneered tops, but careless hands at the factory can obviously still leave marks. I suppose the lesson learnt is not to take anything for granted and always check for glue spots on the body if you are staining. You'd normally sand off any surface glue as part of the basic prep work, but some may still remain if it's soaked in or been pressed into the surface during the clamping the body pieces together process.