I've been fighting with the same issue and tracked the problem down to the following,
Starting a new project with the PIC32MZ2048EFM144 (Same a demo project) and copying all the wolfmqtt_demo settings harmony 3 fails to include
- mqtt_net_glue.c and mqtt_net_glue.h,
- does not update initialization.c netPresCfgs
- does not generate net_pres_enc_glue.c and net_pres_enc_glue.h
Adding the above from the demo causes the project to build ok, (I can't run / test this until I build a PCB with the PIC32MZ)
I then enabled TLS 1.3 support and after fixing errors with needing "HAVE_HKDF" by enabling various SHAxxx & HMAC options this now complies correctly.
I currently have a product that contains the PIC32MX795F512L and was hoping to update this, however all of the above complies to 489k so the PIC32MX is not usable with MQTT + TLS1.3 + USB enabled.
My findings show that although you enable the pres layer and TLS1.3, harmony doesn't enable everything to make things work.
I think the presentation layer issue is a fully blown bug as harmony 2 had the enable encryption checkbox that would then add the flags to include the glue. In Harmony 3 this has been removed and one of the flags can't be set to cause net_pres_ENC_Glue.ftl to add the functions needed to the project.