In general, plant secondary metabolites can have positive and negative effects (Weston A. Price). The reason I don't try to categorically avoid them, but treat them with caution, is that these effects are multiplicitious and biological: very hard to predict what they will do, good or bad...
However, unless we know about the problems with antinutrients, we won't know why eating raw flour or dough is dangerous, why green potatoes are toxic, or how many raw red kidney beans it takes to kill a man (not very many).
But on the whole, unless you are allergic, most antinutrients will be digested, and some are actually good for you. For example, this article mentions that inositol hexaphosphate is a break-down product of phytic acid. Most phytic acid is broken down by digestion, and there is evidence that it can have beneficial effects as well as deleterious effects.
This article points out that most sweet potato antinutrients are destroyed by baking, as opposed to boiling. This FAO article on all the major food crops and their antinutrients specifies that " Heating to 90°C for several minutes inactivates trypsin inhibitors", which explains why baked sweet potatoes are nontoxic. (But the article also points out that diseased or moldy sweet potatoes may have toxins that are not completely deactivated by cooking ....moldy vegetables should not be consumed. Apparently, toxins in normal potatoes are also not destroyed by normal cooking methods. Furthermore, sweet potatoes do not have lectins, but normal potatoes do. These compounds can have some antidigestive effects, but most should be destroyed by cooking.
Antinutrients are important, but I think methionine and nutrient density / glycemic index considerations are more important overall. A few potatoes or slices of bread shouldn't hurt most people, but if you have the luxury of chooses less toxic plant products, sweet potatoes and especially squash and pumpkins are some of the best sources of nutrients, with the least amount of antinutrients.