Tech background:
on this link it explains the techniques and parameters that can be use for manifest merging: https://developer.android.com/studio/build/manage-manifests#merge_rule_markers
One in specific is the tools:node that points out how certain XML nodes on the manifest should behave whilst merging.
Solution:
to achieve some permisions in one and different in other manifest, add ALL permissions you need to the main and in the flavours manifest remove the ones you don’t need, like the example below:
free remove the check license
<uses-permission
android:name="com.android.vending.CHECK_LICENSE"
tools:node="remove"/>