Hmmm, well we just use Bentley for civil road and site design, and AutoCAD Civil 3D, but wasn't aware that either of these could take a load of aerial photos (we often process several hundred) into a single stitched together mosaic. I'm not the CAD guy in the office however, so maybe I need to investigate this. This is where we use PIX 4D to process the photos - so although I don't claim to know how to process the images in the first place, I do know how to use PIX 4D to this end. What happens during processing is all magic (ha!).Bentley software already is a 3d mapping / ortho package in itself, Pix4d would be a lower quality option.
With the level you are working at you already have 1cm accurate ground control points, so any imagery you take will be accurate and give accurate 3d models with what you have.
I have used the Phantom 4 which gives good results and 1cm ground resolution which is good, the Inspire 1 gives a better quality (although you need to get your head round the manual focusing issue), the Inspire 2 will give better results again due to the quality and size of images. However if you don't know how to process the images in the first place no amount of expensive software will wok.
What software are you using to collect the images in the first place ?
And yes we just shoot in easily identified photo points (like a paint stripe corner, whatever) after the photos are taken to within a cm (ish) and then use the utility in PIX 4D to adjust the photo position. Usually 3 to 5 points on an average site dials it in pretty nicely.
Not sure what you mean by "what software is used to collect the images?" We use the PIX 4D capture app to generate a flight plan, correct photo overlap etc.