This is a serious defect with bold transformation (and some others). It would be better to have the transformation work on a percentage of the stroke weight rather than a fixed value. Erwin already knows this, but I suspect that its not trivial to fix. The work-around if glyphs have High Contrast is very laborious.
Probably the easiest method is to do the transformation in several stages. Say, you want to apply a bold transform of 100 funits horizontally and 20 vertically. Set up a transform of 20 horizontally and 4 vertically (and move -4). Apply the transformation to some glyphs only once or twice, and to other glyphs four times.