No. Lens correction profiles don't include centre offset.
Distortion correction calculates a new distance of a point from the optical centre of the image. If you have one process that performs this fron the centre of the image file and then a second process performs this from a different position, then the first process has screwed things up for the second one.
The calculation of lens parameters by Photoscan (and all of the image stitching applications I've used) is an optimisation routine, ie. The end result depends on the data you supply it. Distorted models are caused by the lens parameters optimising to values that are not accurate for the lens. This in turn can be caused by a whole range of factors including inadequate number of images... At different angles... Poor image quality, too low GSD for the expected resolution etc...
You can either use Agisoft lens to calibrate your lens parameters beforehand, or save the lens parameters form a project that has worked well and then load these into subsequent projects.