What are the Oracle Dataguard Implications of Migrating to a PDB?
The notes about this in Oracle 12.1.0.2 state that it is not required to move/copy the files from the primary during the plugin. The note also states that in this release the copy of the standby files of the source can be postponed using the standbys=none clause. This makes it possible to plugin a large primary database in a primary container database and perform redo apply/recovery later, when all files are copied into to correct file structure.

seeHandling of Standby Databases during plugin note 1576755.1

My conclusion is that in 12.1.0.2 the standby files need to be copied but this is not perse during the plugin of the primary database so it does not cause any extra downtime.

Still I would like to see this tested before I would do this on production.