Good grief - there's so many mistakes there. Particularly the use of the Consumer Price Index to price inflation. Should use a Construction Price index. There's no indication which projects include operations, and which are just construction. Which ones include rolling stock, and which ones don't. Which ones include land assembly, and which ones don't. And most importantly which ones include financing costs, and which ones don't.
I’m sorry, but if you had spent more than two seconds actually paying attention, you would have noted that the costs stated are for construction costs only, and that rolling stock has been excluded from costs whenever possible, and that there are special notes for any projects where rolling stock could not be excluded. All of this is clearly stated on the website. This is not some amateur database, these are actual university researchers.
Besides - when the difference between similarly complex projects in high cost and low cost countries is like 4x, 5x, or even 10x, small details like this are not even that important. Financing and rolling stock do not explain a several fold increase in costs.
Your inflation point is also moot. Even if you only look at projects in the last few years, the differences between countries are obvious and enormous. Furthermore, you could also see that inflation adjusted costs in much of Europe and Asia have not increased tremendously over time like they have in North America - to suggest that construction costs naturally increase at a rate multiple times higher than the inflation rate is absurd. Using “construction inflation” is essentially a circular argument, attempting to explain construction cost increases using construction cost increases.
Transit Costs has also done a lot of serious research into finding reasons for certain countries’ costs - among these reasons are having high quality in-house engineering expertise to design and spec projects without political interference, learning from places that produce good results, moving quickly, and encouraging competition, transparency, and accountability. Design specifications need to achieve a balance between overly exact specs (which make it impossible for contractors to find ways to save money) and overly vague design that places more risk on the contractor. There are many other things, but probably reading the actual case studies and reports at
https://transitcosts.com/ is better.
In North America there is little to no in house engineering expertise for large transit projects anymore, and the expertise that does exist is far behind global leaders. While P3s are in some ways a way around this (well managed P3s have produced good results before), I highly doubt that an agency that delivers astronomically expensive projects through P3s would be capable of somehow producing good results through a different procurement process without significant reforms.