Plugin manager does not remove integration plugin overlaps when installing from offline packs

**Logstash information**:

Please include the following information:

1. Logstash version: 8.14.0
2. Logstash installation source: zip archive
3. How is Logstash being run: Via command line

**JVM** (e.g. `java -version`): bundled

**Description of the problem including expected versus actual behavior**:

The plugin manager is not removing integration plugin overlaps when installing it from an offline plugin packs.
The installation process works, but Logstash ends up with duplicate plugins names, loading them by chance and causing troubles.

**Steps to reproduce**:

Example of SNMP integration plugin, please note that `logstash-input-snmp` and `logstash-input-snmptrap` are embedded within this Logstash version:

```shell
# bin/logstash-plugin list --verbose | grep snmp

logstash-input-snmp (1.3.3)
logstash-input-snmptrap (3.1.0)
```

In another Logstash copy, install and generate an offline plugin pack (`bin/logstash-plugin prepare-offline-pack logstash-integration-snmp`)

In the offline Logstash:

```
bin/logstash-plugin install file:///logstash-offline-plugins-8.11.4.zip
```

Check the `snmp` installed plugins:

```shell
# bin/logstash-plugin list --verbose | grep snmp

logstash-input-snmp (1.3.3)
logstash-input-snmptrap (3.1.0)
logstash-integration-snmp (4.0.3)
├── logstash-input-snmp
└── logstash-input-snmptrap
```

Reproduce the issue with bin/logstash-plugin prepare-offline-pack and install file:///logstash-offline-plugins-8.11.4.zip, then inspect the plugin-manager path handling offline packs. Compare bin/logstash-plugin list --verbose before and after installation; done means embedded logstash-input-snmp and logstash-input-snmptrap entries are removed when logstash-integration-snmp provides them.

Written by the indexing model from the issue text.