I've recommended Smart::Comments here many times, but I'll admit to not using it much recently. What you call "The Big Fat Shortcoming" has never been a problem for me; if I need to retain the output, a simple script 2>log has always done the job perfectly. With the advantage over internally specifying a file, that I can do script 2>&1 | tee log | more which I find very useful.

The big limitation of S::C for me is its verbosity. I don't need 4 lines of output for every traced variable; one is sufficient. The way it dumps structures is equally pointlessly verbose. And the cutesy for loop tracing wears thin very quickly. I did start to look at substituting Data::Dump for structures and so on, but them something else caught my attention more and I never completed the exercise.

Like you, I think that the idea of the module, including the source filter, perfectly sound for the purpose, it's just the details that let it down in my view.