Virtually every college performance metric is subject to confounding factors (even assuming every school reports its data honestly and according to the same formulas). That said, the Chronicle/IPEDS financial data reporting formulas seem to follow rigorous and transparent accounting standards (GASB/FASB). They are documented in some detail, at least. For example, have a look for example at the “Instruction expenses per FTE (FASB)” info box on the IPEDS site.
Should we accept a single metric at face value? No … but on the other hand, does anyone here believe the salary differences between Stanford and Liberty University are all down to variations in COL or accounting methods?
As I see it, the endowment, instructional spending, salary, class size, and FA numbers taken together seem to point to pretty much the same set of 15-20 top universities. Not that I’d recommend choosing between ~peer schools based only (or even primarily) on these numbers.