The thing is, I should clarify, that some words have the same first four letters, but those words you mentioned ("Heater" vs. "Heather", "Best" vs "Bestial", "Foreground" and "Forever") have different meanings. This could be why AutoFill is discouraged, if you prefer to create a professional crossword puzzle for submitting to newspapers.
Regarding the "Heater vs. Heather" thing, I also realize that "Heater" and "Heating" have basically the same concept. "Heater" is associated with heat, while "Heather" is a girl's name and also a variation of flower. That said, it's perhaps better to design the crosswords from scratch, enabling the word suggestions when you hover the mouse over a certain area of the grid. Of course, I could use AutoFill, but I would look through the grid to see if there are any words with the same concept that have the same first three or four letters.
It's days like this that I wish CrossFire would update to including the function which searches for duplicate occurrences of the first three or four letters and highlights them upon the click of a button. If no highlighting occurs, the puzzle is acceptable. However, if there are highlighted occurrences, verify to see if these words have the same concept. One time, I found an occurrence of "Box" vs. "Boxes", and that was on Crossword Compiler. This is what I do not want to see in my grid.