In v5 I have three layers that I keep at the top of the sort order by prefixing their names with an underscore i.e. _scratch. It seems that in v6 the underscore is ignored and the layers get sorted by the first alpha character.
My preference would be to allow that underscore to lead the sort order. Having those layers at the top of the list speeds a lot of operations that involve layer dialogs. Most of my heavy lifting is done on those layers then moved to the tree below.