Some of the recipes were submitted by people who didn't fully understand the food lists. You need to read recipes carefully and make substitutions when needed, even if the recipe is listed as being for your genotype.
If you've got health issues, you should completely avoid the "avoid" foods. The idea to "limit or avoid" is advice for people who may not be ready to follow the plan 100% As for the "black dot" foods- you need to avoid them for the next 2 months, minimum. Then try small amounts of one at a time and see if you tolerate each one. Most "black dot" foods are always going to be "eat one serving a few times a year" foods, though others may be considered "neutral" for you personally after you see how your body responds.