You're correct. Function's a own time shouldn't include b's own time, while module's own time will include both.
As of file time, it does not include time spent for parsing itself. Parsing time would be included in include() time. The first file's parse time is to be included in the page total time.

thank you.

could you please try to list some cases (theoretical build ups) that could explain this?

Line time: 1,344 sec
Line time with children: 7,587 ms

you always take into account clock time and not cpu time, right?