I mean that if you use 3 targets to align each before/after chunk pair, and the coordinates of the rest of the targets agree, you will have an estimation of the internal accuracy of the model. If they do not agree then you cannot expect the external accuracy to be any better.
This is a more meaningful way of presenting the quality of the result in terms of 3D coords instead of the average scalebar error.
You do not know how the optimisation works but it was used during the alignment phase anyway; you now need to fine tune it.
There are some points that are flying around, which I do not suppose that correspond to any object, thus they are false matches and should not be taken into account.
I can only see the low resolution thumbnails of the images but the reflections of the lights on the floor are not helping at all...
You do not know which parameters should be checked but some of them were checked and they were initialised to zero;
you should not leave this to chance and at least try to be consistent.
Even if the values change, the same parameter set should be used as you are using the same camera.
Since you are fixing the focus why don't you calibrate the camera so that you have a better initial guess for the parameters values and use it for all chunks?
Normally f,cx,cy,k123,p12 should be fine for a digital camera.
There's nothing you can deduce from the calibration values about the metric accuracy of the 3d model.
The normal case is well studied, convenient when the surface can be assumed to be planar, in which case the accuracy can be assumed to be homogeneous and the images can be easily orthorectified, but is the worst choice with respect to the uncertainty in depth estimation, especially with an uncalibrated camera.
I would also suggest adding images with varying roll angles.
The results should be improved but you shouldn't take my word for it.
Try measuring a planar surface or a sphere and see for yourself.
Having said all that, it depends on the accuracy requirements of your project; if this was gold you were measuring I would not buy from you...or maybe I would
Perhaps you already have what you need but judging from your original post you are aware of the fact that a third party might not be convinced, so you should at least be aware of all the caveats.