There is no functional difference between the two, it is more of a design option.

Security Profile can be overwritten on the BAR file for PEP Node but not for the MQInput Node.

The PEP Node can not be used in a message flow unless the MQInput Node has security settings turned on.

The MQInput Node validates the authentication of the input message before it is processed by the flow. The PEP Node processes messages inside the flow.

syslogs

Trace Node output

Integration Node stderr and stdout

Integration Server stderr and stdout

By selecting the Pattern Target properties from any node any message flow.

Pattern properties must be configured in a Pattern Authoring project before selecting targets.

All properties in a message flow must be tagged for the Pattern Authoring Project to identify them.

By adding a reference all the Node properties are automatically exposed to the Pattern Authoring Project.