Excellent question. I believe the reasons NA-X isn't further investigated, are mostly political.
Native status in America was historically something many people were discouraged from admitting. NA's were encouraged by the BIA to downplay or underestimate their blood quanta for the tribal membership 'rolls', for example; & NA's were commonly, officially & socially classified as inferior, 'colored folk' (albeit "'free' persons of 'color'"), much like Negros & 'Mulattos' or 'Mestizos';
& it remains an 'exclusive' designation, reserved for only a few who are granted certain necessary (though deeply resented & jealously guarded) 'privileges' (due to the circumstances of the invasion of America & displacement/genocide of NA's, by European colonists).
Bottom line: the fewer 'official' or 'bona fide' NA's, the less it ~costs~ the Federal & Tribal governments, lol.
So DNA testing of NA's has historically been mostly about ~exclusion~ from the 'club' (so to speak). I believe that's why the 'experts' & 'authorities' won't admit more than the 'Big 5' haplogroup subclades for NA's. There are ~legal~ & ~economic~ components to the problem of who is or isn't NA. Thus, there is definitely an 'agenda' surrounding it.
(And NA's rarely make a fuss about how we're treated; we've been punished too often, for doing so. Hints: genocide & confinement to 'reservations' which are more like concentration camps.)
The whole culturally accepted 'story' about how America was settled by the many varied tribes we now refer to all as 'Native Americans', is textbook (as if carved in granite); it isn't really open for discussion.
Because if it was, we would learn things about America & its indigenous people that would blow a lot of minds & burst a few bubbles. It would shatter some stereotypes & cost the governments more $$$ & natural resources (land).
The 'Out of Africa' theory of Human migration is a very logical one, based on the enthusiastic, early studies of mtDNA. But its scope has since become ~stunted~ by the same & other political reasons.
And according to the Theory, it should not be at all surprising to find certain geographically specific subclades of nearly all the major mtDNA haplogroups; at least of practically every major Human 'race' & 'subrace': Asian, Polynesian/Indonesian, Caucasian, perhaps Aryan/Indo-European, 'Semitic', African, etc.
The more archaic the haplogroups, the more rarely one might expect to find them represented in the modern NA populations (if at all, since some or many of them may have eventually become extinct in America).
It's already been proven time & again, that NA's have existed in the New World far longer than originally presumed. I would expect that comparatively later emigrants might have fought against the more archaic peoples, perhaps wiping most (but not necessarily all) of them out of the landscape.
But the American subclades should also be proven to be mostly specific to ~America~, due to the varying degrees of longterm continental/hemispheric isolation of the many different tribes here. IOW the longer they've been here, the more specificly 'American' I would expect their subclades to be.
However, the 'experts' don't mention subclades much, when informing NA's who've had their DNA tested, that they're "not Native American" because their haplo~group(s)~ is/are "European" (or "African", whatever).
If you ~knew~ indisputably that you were NA (based on your families' ~oral traditions~ - since American Indians didn't keep written records & later Colonial courthouse records were often destroyed by ~arsonists~);
& you also ~knew~ that you might be 'officially' excluded by self-made, government funded 'experts', based on shoddy, mickey-mouse 'science' - would you care to have your DNA tested? I think not.
And do I consider these reasons "nefarious"? Was the genocide of Native Americans "nefarious"? Lol.
I realize my views on this subject may be unpopular or politically 'incorrect'; but I must tell it as it is (or, at least as I see it). And my point of view on the matter is quite relevant to this discussion of DNA/Genealogy.
[UPDATE: This reply wasn't 'approved' by the Moderator (R1a1a, presumably); & the OP was deleted from the forum. They will allow all sorts of political / social discussion, as long as it has nothing to do with Native America. $$$ They are protecting their interests, is the logical conclusion.]