I know that their reason was not to favour one city/state over another, but isn't it the same with the newly founded capital?
The new capital cities keep one region from being favored over another: the USA's northern states vs. the southern ones, or Australia's New South Wales over Victoria.
Imagine that the Acts of Union was between two nations on equal footing. A capital for the new kingdom in either Edinburgh or London favors one of the merging states over the other.