There are not the "Present Continuos" in yours examples, if I'm not mistaken

"by + present continuous" is a good and natural way to describe a method or process, just like in the examples you mentioned. If you omit the word "by", you don't clearly express that the following verb form describes the method or process. e.g. (no "by") Fortunately, the compiler helps raising an error when you accidentally use a value type for the lock statement. This is wrong and doesn't have a clear meaning. I might guess that the writer meant that the compiler first helps and then raises an error or that he "helps to raise" an error. "by" ensures there is no ambiguity. So "by" is essential for the construction. "Through" is sometimes used instead.

You have to use 'by' in order to express the process of the verb + ing, An alternative would be to say 'through being' or 'through ensuring', but your sentences will not make sense without one or the other.