Currently, Inventor does have this functionality built in to it, but it has a lot of issues that need to be worked out. Mainly, if two (or 500) parts have the same part number, stock number, unit type and physically all other parameters are the same with the exception of the length, MERGE the items!!! Who cares if they reside in two separate phantom subassemblies, those subassemblies were made phantom for a reason. Obviously if you didn't want these parts to be calculated together, you would not go through the effort to make the assemblies phantom in the first place.
This is extremely frustrating Autodesk, and should have made it into one of your most premier design software's by now.
Sometimes it just makes the most sense to have some of these length quantified parts reside in a subassembly. Make it so.
