I feel like I am already doing most of those things with exception to the class. 

I already have customers and subcustomers set up. We're talking about hundreds of customers, so creating separate asset accounts for each one would make my balance sheet unwieldy at best. The journals already have transaction lines segregated by customer (with customer:subcustomer in the Name field). Is your solution is to put the same information again in the class field and then total by class?

By the way, I have found this same issue with checks or bills with multiple lines assigned to different customers/subcustomers. It only displays in one on reports.