Apply-PnPProvisiongTemplate on Modern Site Referenced content type not available in site or in templ

I guess what you're already suggesting is indeed the case. Content Type syndication from the hub seems to be processed asynchronously for modern sites instead of synchronously for classic sites. This is one of the reasons provisioning of modern team sites  is so much faster than provisioning of classic sites.

I don't consider this a bug in the PnP Provisioning engine. My suggestion is to extract your Content TYpe and Field definitions (schema XML) from the hub and include it in your Provisioning Template XML so that you have the Content Type available while provisioning and you're able to associate it with your library. Eventually the Content Type will be syndicated from the hub with updates made (if any) after you extracted your definitions.

Hope this helps!