Zip files have all the metadata in a footer rather than a header. As a result, compressed files can be added and overwritten by appending to the file without disturbing already compressed data. Additionally, the "deflate" compression likely does not span across files, so files that did not change from version to version would have a similar compressed byte sequence, regardless of the order they were added to the archive.

I'd argue that zip is a relatively simple compressed archive format. Its simplicity is its charm and the reason it's so popular. More space-efficient algorithms would be less likely to be "patchable" as there would be less redundancy / structure in the compressed representation to exploit (the best compression seems like it would have similar properties of random data.)