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Interesting question! You are certainly right that all of the listed disadvantages are specific to the developer. I would suggest, however, that a disadvantaged developer is far less likely to produce a quality product. There may be no runtime disadvantages, but imagine how reluctant a developer will be to make small changes if each compile takes hours (or even days) to complete.
I would look at this from a "premature optimization" angle: modular code in multiple files makes life easier for the programmer, so there is an obvious benefit to doing things this way. Only if a specific application turns out to run too slow, and it can be shown that inlining everything makes a measured improvement, would I even consider inconveniencing the developers. Even then, it would be after a majority of the development has been done (so that it can be measured) and would probably only be done for production builds.