The scripts do not use the funits/em setting. The scale is by a percentage, but the bold transform is in funits.
Almost all of the scripts will need manual adjustment to suit each font. They were designed using my Verajja font (derived from Bitstream Vera), and won’t be right for other fonts.
The scaling is intended to adjust to counteract the effect of adding vertical funits to the horizontal strokes, and the move is intended to maintain the baseline position.
Serifs, or any thin strokes, will be much too thick after a bold transformation because the transform is absolute, not proportional.
It would be better if it used percentages
If you regularly work with Mac fonts @ 1000 funits/em I suggest fixing them first to 2048 funits/em.
Resizing Fonts and Changing Units per em values
Or, just save all of the transform scripts as new scripts for Mac, or overwrite the existing scripts if you seldom work with 2048 funits/em fonts (which are by far the most common on Windows).