Sure, I don't disagree that webpack merely brings those features together into one place. But webpack was born because 80% of the time you make a webapp you don't want just minifcation, or just transpiling, or just cache busting file names, or just file event based recompiles, or just bundling, or just tree shaking, and on and on. Most of the time, you want all of that stuff. People got tired of maintaining their 1000 line npm/gulp/grunt task files, so a bunch of projects were launched with the goal of eliminating that glue code. Webpack is the most popular, but there are of others like Brunch or more recently, Parcel.
I think webpack is a mess, but will probably end up being the mess we're stuck with for sometime, because while it is complicated, it does solve a lot of problems. I see a lot of parallel with the GNU make and autotools setups used to build most C projects. The layered way that autoconf, configure, and make build configuration to compile and install programs is pretty complex (to my eye). Sure, it could probably be simplified a bit, but cross compiling code that dynamically links to libraries and installing it on different operating systems is just a complex problem.
I use and am very happy with Brunch. Yes, Webpack might have more features but my Brunch config is like 25 lines and it just works. It took me fifteen minutes to set up having struggled with Webpack for a couple of days.
Most of the things you described live outside of webpack, and webpack is NOT required to use them.