No, the Plugin Portal is a superset, not a subset of JCenter. Some requests end up going to JCenter, but there are JARs and POMs in the Plugin Portal that are not available directly in JCenter.
I was specifically addressing this point. There are JARs present, but not for every POM present. Some POMs reference other artifacts which are only on JCenter or only on the plugin portal. You would need to follow the dependency trail to see exactly which is the case for a given plugin. However, the plugin portal handles this transparently to the end user.
For Gradle plugin access through Nexus, setting up a proxy repository to https://plugins.gradle.org/m2/ and using that as the repository in buildscript or pluginManagement is enough. There’s really no way to tell what’s wrong with what you’ve provided. With what you’ve provided, your issues seem most likely environmental or in Nexus.