Currently in pegasus 4.9 registration gets automatically turned off it the user has not defined pegasus.catalog.replica property
In 5.0 release we are pushing for zero configuration for users where possible. hence usually the pegasusrc is empty and as a result no registration jobs are created for the workflows.
One proposal is on table is for us to create a separate output replica catalog in the user submit directory that is different from the input replica catalog. If a user does define pegasus.catalog.replica properties then the user defined will be used for registration.