AncestryDNA, 23andMe, and Family Finder each include two separate tests (auDNA and X-DNA). X-DNA has a distinctively different inheritance pattern from auDNA.
It certainly causes additional clutter when a tester reports they tested (their auDNA and X-DNA) with multiple labs. A possible solution is for the instruction/help page to recommend that auDNA testers only report one auDNA test and one GEDmatch ID. In the note field for their auDNA test they could mention other labs they have tested with.
The chart at http://www.wikitree.com/treewidget/Roberts-7085/89 shows the little X that should be used. My first thought was to have a separate list of X-DNA relatives (in the way that Y, mt, and au are listed separately). But I wonder (in order to avoid clutter) if it is possible to include the little X on the left side of the au for the X-DNA relatives of the profile that a user is looking at? Only some of our relatives who are likely to share some of our auDNA are able to share some of our X-DNA.
I want to avoid (put off) the haplogroup categorization issue. I can only imagine it working if the ISOGG Y-Tree and phylotree had persistent links (urls) to the SNPs (which defined haplogroups) within those trees. That would allow one to know where their haplogroup fits in the hierarchy as the tree changes as new discoveries are added.
I don't believe the solution for X-DNA or auDNA can connect with what is done with haplogroups because auDNA and X-DNA don't have haplogroups. 23andMe and the Genographic Project report Y and mtDNA haplogroups but they have nothing to do with auDNA or X-DNA.
I believe the long term solution for auDNA and X-DNA is to automatically show the shared ancestry for people who all share the same auDNA (or X-DNA) segment with each other. Then it will be much easier to confirm each of their ancestral lines back to their shared ancestor (or ancestral couple). That is to say to have GEDmatch, or DNAgedcom, or DNA.Land allow a url which links to the tester's ancestry such as WikiTree's Relationship Finder or compact family tree.