The built-in PK3 files aren't optimised.

[tomatopipps]

I was looking through gzdoom.pk3, and I noticed it's compressed using only the DEFLATE method.
There is a program included in zdoom's (and therefore gzdoom's) source code called "zipdir" which automatically chooses the best compression method out of DEFLATE, BZip2, and LZMA. It was created specifically to optimise zdoom.pk3. Why not use it for the release builds?

[Gez]

Because sometimes it's useful for people to look at what there is in that file, and the optimized zip compressions are not supported by many utilities, so people complained.

[Graf Zahl]

The main reason was that the Doom editors had problems - and they need to be able to read the file. That's more important than saving a few bytes.