Message modificaton modules modify the message object, so the next actions can process the modified message. However, if the action that invokes the message modification module runs on a real queue (anything other than queue.type="direct"), the message object is actually duplicated, and done so only for executing the action. In other words, the duplicated message object is immediately destroyed after the action completes. That means the modification made by the module will never be visible by anyone else.
So never run a message modification module on a non-direct queue. Message modification modules usually start with the letters "mm" (as in "mmjsonparse").
Note that this is not a bug: rsyslog’s design is generic, and for most other actions the duplication of message is necessary in many cases. The config parser detects this kind of problems, but does not auto-correct it as the issue points to a potentially larger issue.