I’m not sure if it would make a difference since we use linear registrations in these steps. My feeling it that rather the risk of failed coregistrations increases if one has multiple cascaded registrations. But I don’t have any data to support this claim.
I think the “brainshift correction” tool in Lead-DBS should remove any pre- to post inaccuracies, especially if using good quality data.
Regarding postop MR vs. postop CT, this is an ongoing debate and I have not decided. I used to prefer MRIs over CTs since one can verify position in native (postop space), sometimes directly identifying the STN or other structures. I guess the advantage of CT is higher resolution re placement of each contact of the electrodes. Although one can visualize them with multiple MRIs, pretty good as well.
Hope this helps?