There is a two-fold relationship between extractivism and indigenous peoples: on the side of formal law, rights and the State, there are international contracts like ILO 169 or the UNO text on indigenous peoples from 2008. Those define a basic framework - that does not work always. On the other side are the indigenous peoples, many times with the background of a decade-long fight for their rights.

Now, in countries where both extractivism and the indigenous movement are strong, you have a legal framework that includes a (sometimes not even binding) obligation to previous consent with the indigenous peoples in place. And an indigenous movement that wants much more, namely, again in the cases of Ecuador and Bolivia, to have complete and utterly control over their territory and the natural ressources there. In this latter perspective, extractive industry would have to work with indigenous legal systems. Only, I do not know a single case where it works like that.

Extractive industries are dominated by transnational corporations (TNCs).  Effective control of TNCs by Westphalian nation-states is problematic, so the TNCs are unlikely to submit to any indigenous regime of regulation or even negotiation from a standpoint of equality.

Other entities involved in extraction are, in a sense. alter egos of Westphalian nation-states: PEMEX in Mexico, Petróleo Brasileiro in Brazil, Yacimientos Petrolíferos Fiscales Bolivianos in Bolvia.  Some people would add Gazprom in Russia.  As to such alter ego entities, from the indigenous point of view, to deal with them is to deal with the nation and legal pluralism within a specific nation is what it is, with no exception for these sorts of transactions of which I am aware.

International legal conventions, national legal conventions (including those where, as in the US, indigenous populations are usually regarded as domestic dependent sovereigns), the organic law of the indigenous nations themselves, and the laws of the provinces/states (in the US) in or through which indigenous sovereign boundaries may exist all supply a legal and regulatory framework under which extractive industries operate.  Self-determination initiatives among indigenous populations with regard to regulating the extraction of natural resources within their boundaries is increasing, and is also increasingly beginning to shape the policies of the larger/dominant government entities.  The subject is huge, fraught with conflicting currents, and subject to jurisdiction-by-jurisdiction differences that may not be generally applicable or particularly instructive elsewhere.

De conformidad con el Convenio 69 de la OIT, los pueblos indígenas tienen derecho a participar en la toma de decisiones relacionadas con su entorno y con cualquier cuestión que pudiere afectar su forma de vida tradicional y sus territorios ancestrales.

El reconocimiento de la multiculturalidad y el consecuente derecho a la preservación de la cultura que tienen todos los grupos humanos,  me parece que es un derecho humano de máxima prioridad, sobre todo si se le confronta con derechos relacionados con la posibilidad de hacer negocio de una empresa, de manera que en caso de conflicto debe prevalecer el derecho a la preservación de la propia cultura que tiene el grupo indígena, contra el derecho a la explotación económica de un yacimiento minero. 

In terms of legal pluralism and its comprehensive and huge influence of the modern political, socio-legal realms, narratives and trends I will offer you some newest articles covered issues you want to find pertinent answers. 

TURKULER ISIKSEL and ANNE THIES (2013). Changing subjects: Rights, remedies and responsibilities of individuals under global legal pluralism. Global Constitutionalism, 2, pp 151-159 doi:10.1017/S2045381713000117

TURKULER ISIKSEL (2013). Global legal pluralism as fact and norm. Global Constitutionalism, 2, pp 160-195 doi:10.1017/S2045381713000130

ROBERT MCCORQUODALE (2013). Pluralism, global law and human rights:

Strengthening corporate accountability for human rights violations. Global

Constitutionalism, 2, pp 287-315 doi:10.1017/S2045381713000099

Por error de mecanografía en la respuesta que dí me referí al convenio 69 de la OIT. El convenio de la OIT al que me quería referir es el 169. Una disculpa