Quite a number of config things that we have can/do reference content entities:
- Blocks of Custom Blocks (required, per block instance)
- Default values of image/file/term/entity reference fields (optional)
- Aggregator feed blocks (required, per block instance, reference feed ID)
To reproduce this problem in the most "awesome" way that core can offer:
1. Create a new custom block type
2. Create a custom block of that type
3.. Place that block somewhere.
There is now a block config entity that depends on a custom block content entity which depends on a custom block type config entity.
Now, go and deploy this. Good luck.
I have no idea :) We have no system in core for syncing content.