The answer for the moment is that the MoD are still in discussions regarding how service personel will be treated. There are similar discussions with other public sectors.
I understand that it will make zero difference to service personnel posted to Scotland as there is an established precedent of where we theoretically live for tax purposes. For those with direct links to Scotland (place of birth, established family links, home owner, spouse liable for Scotish taxation etc etc) things are less clear but the rumours out of MoD is that the status quo will endure. It has been rather quiet on spouses though.