The impact of the Bayonne statute on Meztisos & Native Americans

In between the time Boney & his bro promulgated the Bayonne statute and when the various Latin American wars for independence happened did the indigenous & Meztisos gain more rights because the statute took away the privileges of the peninsulares or did the natives & mestizos have less rights due to the statute limiting the power of the church which was the only institution that acknowledged their rights to a meaningful extent?