Symptoms
What are the differences in upgrade process for Wordpress between when Wordpress Toolkit is enabled and when it is disabled?
Resolution
WordPress Toolkit detects installed Wordpress instances. It does not matter if the instance was installed from APS catalog or manually.
When you press Update, WP Toolkit initiates searching for available updates for each instance directly using native methods. Each instance will then look for available updates from wordpress.org using curl requests. APS application upgrade will not be performed in this case. This means that APS controller's notion of installed version will differ from the actual version therefore giving inconsistent system.
If WordPress toolkit is disabled then all APS WordPress instances will be upgraded during daily maintenance script execution in case a newer version of application is available in application vault (or in APS catalog) and auto-updates for this application are enabled.