Hello Shaun,
Since you are using Sequential pre-selection, you wouldn't get matching points for the images from the different lines of "space invader" or "pick up sticks" scenarios or from different radius of "spiral" scenario.
If you are using "space invader" scenario and have hundreds or thousands of images, it may be reasonable to align the data in two iterations: with sequential preselection and then with estimated preselection, providing that most of the cameras are properly aligned.
As for the mesh reconstruction - using Sparse Cloud source would give you very rough model, so you may consider building the model from the depth maps with medium/high quality in Arbitrary mode. As for the texture reconstruction, I can suggest to generate it in Generic mode and then in the model view switch the view from Perspective to Orthographic, then orient the viewpoint in the desired way and use Capture View option get a kind of planar orthomosaic projection for your model.
If you continue getting many not aligned cameras in the project, please share the original image data to support@agisoft.com.