Two differences seldom mentioned are:
1) field of view for the 100mm lens is about 1/2 that for the 50mm lens so when the object is at the same magnification, the 100mm's background is only 1/2 as wide as that for the 50. Therefore it is a little easier to compose in a way that avoids distracting backgrounds - just like the diffference between normal telephoto & wide angle shots.
The left photo was with a 50mm macro lens, right with a 90mm macro lens, both f4, same geometry.
Notice that the increased magnification of the long lens' background also makes the background look more out-of-focus; this is important when you want to isolate the subject.
2) it is twice as hard to hold the 100mm lens steady than the 50mm lens at the same magnification & f stop.The effective focal length for the 1/f speed rule is actual_focal_length times (1+magnification).
A Dave in Iowa