Absolutely agree.
When we prepare a Business Case to justify putting in a new system or to enhance one we do need to include the operational costs, here called "long-term application costs". In fact, a lot of what Jeff Relkin is talking about is building the business case.
Before we embark on any project we (with the business owner) need to identify what we are trying to achieve and justify why this project is needed (#9 and #10 in Jeff's list).
The justification will include the cost of doing the work (#4) and on-going costs, sometimes called "total cost of ownership" (#1, 2, 3, 8).
These costs may be reduced by various measures (#5, 6, 7).
A lot has been written on estimating work effort. Jeff has identified a very important practice: keep track of what you have done. This provides historical data which can be used as a starting point for future estimates, which enables us to become better at estimating similar work in the future. Use hindsight!