Two different build merges as one

This is actually two different questions.  The first is how to share IP without sharing source files.  The second is how to communicate between the HPS and a Nios.  I'll address the first and let someone else address the second.

There are two methods for the vendor to share their design.  The first is using partitions and exporting a partition netlist.  You can find more information at the following URLs:

How can I create a design netlist without including my source design files? | Altera Community - 341619 

https://docs.altera.com/r/docs/683247/25.1.1/quartus-prime-pro-edition-user-guide-block-based-design/answers-to-top-faqs

You can find training on block-based design here: https://learn.altera.com/learn/learning-plans/82/altera-quartus-prime-software-tools-features

The second method is to use IEEE 1735 encryption of the source files.   You can find more information in the Quartus Prime Pro Edition User Guide Getting Started document at the following URL:

https://docs.altera.com/r/docs/683463/25.3/quartus-prime-pro-edition-user-guide-getting-started/support-for-the-ieee-1735-encryption-standard 

I hope this helps!