Hi syaguma
If you set the "Make REST API calls with Read access" to GRANT for a particular role at the root node, then it would be set as GRANT for all the sub nodes by Default. But you change this permission explicitly for a sub-node by changing permissions on that particular node.
A better way to this would be to change permissions only on Sub nodes and not on root level until and unless we want to grant Permissions at the Root level.
The Read Access permission is used to set read permissions for categories, boards, posts etc and it would not impact the read access to the API user.
