Mapping accuracy

The data collection and overlap all look good. Usually we get to within a pixel or less in the alignment but the vertical numbers depend on the accuracy of the model and the accuracy of the collected points. 

Since we don't know how good or bad the elevation accuracy is and have no required for any specific number all we can do is minimize the vertical error among all the points using the the shape of the original model that was calculated. Essentially, we don't change the shape of anything for the realignment other than to match the GPS locations in latitude and longitude. This is why we don't offer any of the 3D outputs on the reprocessing. Only that image based products are realigned. You will likely want to use client software on your computer if you are really trying to get a solid RTK accurate result. Things like that take a lot of touching and knowledge to do properly. 

For volume measurements this almost never matters since those are relative measurements. The general shape of the model is accurate in relation to itself over short spans. If you are looking for absolute accuracy you will likely need to get good at doing a lot of this by hand/manually. 

Since your site slopes pretty considerably from one side to the other you might want to use Terrain Awareness to track that and get consistent 80% overlap throughout the scene. Also, having large areas of bare trees on all sides isn't helping anything. You will get better results sticking to solid surfaces. 

Thanks for the reply Zane.
So would the elevations within a pile be relative to itself? I need to extract some piles and create a base surface because they are piled against a wall. I'd like to create tin files using another program.
I know how to georeference and image using Arcmap, but how would you adjust for elevation?

I've been trying to make sure I get enough coverage on the sides so I can get a reliable model, hence the trees. Is there another way to achieve that?

Yes, the pile volumes will be fine. Volume measurements don't matter if the whole model is up or down 100 meters. It is all being measured relative to the base. 

When things are piled against a wall you will have to use custom tools but the if the whole thing has an offset it won't make a difference to the relative measurements. 

If you have to measure something that is right next to trees then it can't be avoided but avoid it if you can. It still probably isn't changing much for single pile measurements.