Bundling and minimizing can very significantly reduce code size, by eliminating unused code.
This is beyond the stripping comments, whitespace, renaming all symbols to short identifiers, replacing idiomatic constructs with shorter equivalents, etc. that people expect minifiers to be doing.
Bundling with tree shaking can get rid of a lot of code that would otherwise need to be downloaded. This is especially the case when using only a subset of functionality from a larger library.
Otherwise, for most libraries, if you pull in a single function, every single module from that library will also get loaded. This applies both the pre-bundled libraries (i.e. where there is only one large module, so obviously everything gets downloaded), and non-bundled libraries, because most libraries have you import from an "index.(m)js" module, that exports all the various public API of the library. Which means a browser with import maps will need to download all those files, and all files they import, which will be basically every module in the library.
Minimizers themselves often also have some sophisticated dead code elimination. Indeed, one potential (but inefficient) way to implement tree shaking is simply to bundler without shaking, while using module concatenation, and then simply passing it to a minifier with good dead code elimination capabilities. This would be able to eliminate basically anything tree shaking could, and more. The more comes from both from any eliminable code the bundler would not know how to eliminate, but also being able to eliminate anything that was only imported by said dead code.
This is one of reasons why uncompressed minified code can sometimes beat out the compressed original code, and is still at least somewhat compressible itself. Of course I have not even touched on having fewer files to download (which still has meaningful overhead), nor the smaller resulting codebase being faster to parse than the.
Lastly, but not least, many people want to use typescript or jsx when writing their code, which means the code needs to be pre-processed before a JavaScript engine will read it. If you already have a compile step, then adding bundling and minimizing on top of that can be relatively simple and make good sense for the above reasons. (Note can be simple. It depends a lot on what tools you use. Webpack for example can get really complicated, but it also offers some really powerful features.)