Leveraging multiple SF ID's within 'Company' MDA and other MDA data

We have a unique scenario where our individual lines of data can apply to multiple customers as our customers have relationships with each other. This has caused some issue in various aspects. Here are some examples:

1. We need to have different C360 sections to account for pointing to the two different ID columns. 
2. Rules need to be written twice to pull from both account fields making management of the rules more difficult. 
3. We have partners that are listed on the customer's Account Page but are unable to establish a 'look-up' on the company object without Gainsight being confused as to which ID to pull from (click on the customer's name will pull up the partner's page instead). 

Is this something that is unique to our org or do other users struggle with this as well?