How can one demonstrate/assure safety for LRU's, CBAs, SoC's and other integrated modules?
Yes, I've had some experience in dealing with complex hardware certification both with DERs and with FAA ACOs.  For the last 15 years or so, the process has been well defined as both FAA and EASA have adopted RTCA DO-254 Design Assurance Guidelines for Airborne Electronic Hardware.  

I haven't run into many cases where there are any meaningful difference in interpretation of the guidelines, especially when discussing internally developed components.  There are some differences in what a DER/ACO will accept when you attempt to use commercial off the shelf (COTS) components.  DO-254 section 11.2 covers the use of COTS components but as it points out, the issue is lack of design data from the developer/manufacturer.  So coming to agreement on what is acceptable for these cases is highly variable depending on the DAL required and the available data.  

For higher DAL levels it's getting harder and harder to get approval for COTS. You also have to deal with the fact that COTS parts may go through significant design changes on a regular basis.  That will impact your ability to maintain a single configuration.  Every part change has to analysed for impact and the configuration and certification updated.  That constant churn can quickly overcome any savings in procurement costs.

As to the more generic question of consistency between ACOs and DERs, it's an ongoing discussion within the FAA.  They want consistency but they don't want to to be so restrictive that all decisions get made at headquarters.  Every DER  or ACO I've met has had their individual biases and technical areas where they are comfortable.  So in that sense, there's always a bit of luck in getting one that sees things your way.  I don't think that will ever change.