I'm aware of the changes to the first layer height and the ongoing discussions about the recent changes related to using the z-offset for first layer squish. However this post is yet another issue regarding first layer height.
When no raft is used, a value over 100 results in how the first layer is sliced, not just how much extra filament is used. So a first layer height of 200% on a model with a .1mm layer height is actually one layer less. The final height is the same but one fewer layers. The first layer is sliced and printed at .2mm
When a raft is used, a value over 100 results in the first raft layer (already quite thick on purpose) printing at a thicker size but no change to the rest of the raft or slicing of the model.
This discrepancy may sound nit-picking, but due to the way I model miniatures for release to the general public it definitely results in a lot of confusion.
S3D support, If nothing else, better documentation would go a long way to helping your customers with this product.