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You will have to report errors on tools one by one, and some
of them may not be fixable. From this report, it is not
clear what precisely the error in IDLE is.

In any case, the behaviour that the .pyc compiler embeds the
source file path cannot and will not change. The mechanism
for __file__ is different because __file__, for a .pyc file,
refers to that very .pyc file, not to the source file. OTOH,
the debug information refers to the source file.

If the .pyc file says the source is in
/rfs/proj/cse/scripts, you should arrange that the source
file really is in that location. If you move the files to a
different machine, you will need to delete the .pyc files.

I do not completely agree that the traceback is erroneous.
If your complaint is that it refers to a non-existing file:
this could be fixed by not printing the name of the file if
it doesn't exist. However, I would not think that this would
be an improvement.

If you think that the traceback should magically guess where
the source file is: this is not implementable in a reliable way.