Yes, they're private companies, and they do diversification like investing in real estate around their rail cooridors to grow towns and grab people looking to do some shopping in their adjacent department store as passengers are walking through the stations. This is transit-oriented development at its best. (Also, ask google why land property lines in the US western states often look like big checkerboards)
But there's no mention of the Japan Railway Construction, Transport and Technology Agency (JRTT). That's the government entity that builds many new Shinkansen lines. It then leases them to the JR companies at a fixed rate for 30 years. This keeps massive construction costs off the private companies' balance sheets.
Or when they do need large capital spends, there's no mention of the Fiscal Investment and Loan Program (FILP) which provides loans in the form of low-interest credit backed by government guarantees. Their creditors are effectively lending to the Japaneese government, not the JR company.
Is that kind of system really privatized? It's hybridized at best, and it shows that you really need government support of some sort to push country-scale infrastructure like this forward. Sorry free-market absolutists.