IMO, it is much more important, in the chambering alignment, to dial in off the lands. The lands are the result of the drilling and reaming process, not the grooves. The grooves are generated from the tool, button or cutter, that is guided off the original bore, which is the lands. The chamber reamer pilot guides off the lands, not the grooves.
All that being said, sometimes I cut a micro-bevel on the crown. This is a bevel that just cuts from the lands to the grooves, about 0.002" X 45 degrees. If I am cutting a micro-bevel, I indicate off the grooves off that end only.
Why a micro-bevel? It makes the crown much less subject to damage from the cleaning process, and if properly cut, it does not harm accuracy.
Generally though, if your lands and grooves are not concentric you have a crappy barrel anyhoo!!