This is a very sensible list. With Madison as a high quality match, I’d consider applying EA so that if your daughter gets in, she can apply to the Honors program by the priority deadline in late February so that she will have a decision in Mid March to compare against other RD choices, assuming she doesn’t ED or is not accepted ED anywhere.
If Rice is a clear first choice and is affordable, then go for it. If she likes the feel of a residential college system, she should also take a look at Harvard or Yale. They will be greater reaches than Rice, but they are also SCEA vs ED so she and you can preserve your options even if she gets in. Just looking at the profile you put up, I think she has as good of a shot at either school as any unhooked applicant who didn’t win some recognized national/international award.