There are different ways to organize the structure. And as other say in this Stack Overflow post, it depends on the plugin and what it does.
It is good to test what works best in terms of having things organized in order to find easier and maintain code.
As it happens with coding, sometimes you start with just a few lines of code and end up with hundreds and a few files to include and then there’s the classes and the styles, and, and, and.
This reminds me how it goes with any type of project when the scope becomes not so clear. And this may be in part because of the many parts involved not understanding the technical parts and what it really takes to make structural or functional changes.