As I understood, you base64 the zipped data on input and the other way around on output.
The reasoning being that the base64'd binary data is safe from being corrupted when the file is edited in text editors, as a response to the warning stated on the last paragraph of the original post.
The idea is to first zip the binary, then base64 the zipped data. Conversely, the script first decodes the base64 to a zipped binary, then unzips the binary.
It's just to mitigate the wastefulness of base64 encoding. You end up with a file that is text editor friendly and not quite as bloated as directly encoding the binary would be - but of course the file is still larger than simply appending the binary directly like in the OP.
Also, if you don't care about text editor friendlyness, you could indeed just zip the binary and then append it to the script for an even smaller file.
The reasoning being that the base64'd binary data is safe from being corrupted when the file is edited in text editors, as a response to the warning stated on the last paragraph of the original post.