Is the Regalian doctrine enhanced or diminished?

Years ago, the Supreme Court was confronted

with the issue: whether ancestral domain should be recognized as a legal category in Philippine
jurisprudence. Let us begin where it began.
The Novisima Recopilacion de Leyes de las Indias started it all. The Spanish Crown put it
thus:
We having acquired full sovereignty over the Indies, and
all lands, territories, and possessions not heretofore ceded away by
our royal predecessors, or by us, or in our name, still pertaining to
the royal crown and patrimony, it is our will that lands which are
held without proper and true deeds of grant be restored to us as
they belong to us, in order that after reserving before all what to us
or to our viceroys, audiencias, and governors may seem necessary
for public squares, ways, pastures, and commons in those places
which are peopled, taking into consideration not only their present
condition, but also their future and their probable increase, and
after distributing to the natives what may be necessary for tillage
and pasturage, confirming them in what they now have and giving
them more if necessary, all the rest of said lands may remain free
and unencumbered for us to dispose of as we may wish.
Thus, was asserted the Regalian doctrine. The Spanish King claimed ownership of everything of
value in the Indies or colonies thereby stripping natives of their ancestral rights to land.
Philippine courts, all the way to the Supreme Court even after the arrival of the Americans,
followed the regalia doctrine.
Then came Carino vs. Insular Government, a decision penned by Justice Holmes,
reversing a decision that had gone all the way to the Philippine Supreme Court. The case
involved the claim of a native Ibaloi to ownership antedating colonial times. Whereupon, Justice
Holmes ruled in favor of Carino and ordered the registration of the 148 hectares in Baguio in his
name. Justice Holmes recognized that he had native title to the land. Can ancestral domain and
regalia doctrine stand together?