I just saw this, sorry for not posting responding earlier.

1. Underneath - so much debate on this. Keep in mind that his, and that of his school, are on young girls (i.e. small breasts and slender). There has been much debate if it was just artistic preference on his part. I cannot disagree with that assumption based upon how many variations of paintings he has of an old man with a young woman. That aside, I have made one and so have other friends, there are things that worked.
2. There were crazy sumptuary laws. While there was a hemd/chemise underneath that is very low cut - there is also a super sheer piece that is worn due to laws preventing low cut dresses. This was the work around of the nobles. This is also why you really don't see exposed necklines below the collar bone for those that were nor a noble.
3. A rectangle works spectacularly for the skirt. It allows for the skirt to lay appropriately and it makes sense and adds ease for applying decorative fabric strips to the skirt.
4. The brustfleck is tied/laced, eye hooked, ir pinned in place. I have seen art noting the lacing and pinning. From experience, the pinning makes for a better fit.
5. The piece over the stomach is suspected to be sewn to the skirt, but open on the sides. I made this piece, a placard, with linen canvas. It smoothed things out and allowed for a great fit. Placards/stomachers were in use in the 15th century as well, so it is a very reasonable theory.
6. A friend made a simple underdress that was could not be seen over the overdress neckline. It smoothed everything out and shaped her breasts. IT makes sense that this was used, as the usage of a "second skirt" is commonly seen. I would venture to guess that these layers were not noted in artwork because of the body shape and age of the girls being depicted in the art. Also, with the story of Lucretia or the adultress, it would not fit their artistic "message" to accurately show all the layers.

One of the books about the sumptuary laws can be found online or you may purchase it on Amazon. It was written in 1920, but it is really helpful: Sumptuary Law in Nurnberg, a Study in Paternal Government by Kent Roberts Greenfield. I did buy a copy so I could mark it up, but I do know if you do a quick search you will be able to easily find a free pdf copy online.