I can't see them being flexible about this. Like Grinity said, the computer can score the scantron. One way to help ease DD's mind about filling in the wrong bubble is to let her use a "marker" (a piece of paper that covers up some of the other questions and allows her to put it just under the one she is on. Our school has the lower grades do this to make sure they are all in the right spot.
Another reason they can't write in the book is that some questions require mental math, without the use of scrap paper. There are even rules as to how many times the questions can be repeated, if at all, so, again, I can't seem them allowing it.