Unfortunatelly, associating a persons name with the source was a bad design decision by that software company. Software companies make bad design issue all the time. Usually they fiix those issues or people relize the error and move to software that does not have that design issue.
Sorry, however I will strongly disagree with you. If a census reports a surname as 'Smythe' (normally Smith), I much prefer an accurate report that states 'Bill Smith was enumerated as Bill Smythe in the xxxx census'. Knowing of the use of a different spelling for a specific period means I check other record sources (especially during that time period) for the alternate spelling.
So no, the different spelling is not a 'design issue', but is a way to record and report the use of a different spelling and the circumstances of that different spelling. To not record that difference is the error.