It does not matter by how the images are obtained. It is very helpful if the images are georeferenced but it is not necessary.
If you use targets with RTK data, very precise models are obtained. It's ideal, everything depends on the needs.
These two programs are able to work with almost any photo file format, no problem in that regard.
The difference in price, 3500 or 6500€ is due to the difference in quality between both applications, functionality and ease of use. Initially Agisoft was a 3D modeling program and not photogrammetry. It has evolved over time. Pix4D was born focused on photogrammetry. I have the Pix4D and I haven't used the Photoscan. Googling a little bit on Google you find comparisons that will help you decide. When I looked at it, the vast majority of people said it was better Pix4D and that's why I decided for it. I can't help you in that way more than that, I'm sorry. Seek opinions from users of both programs and decide.