Yes, I see what you mean now. I didn't check .zip contents at all, my mistake.
Yes, this was definitely uploader's preference.
Since you ask, I do prefer .zip myself, which is the default that programs like RomVault and ClrMAME Pro are doing.
If you want to convert all those unpacked files to packed, probably RomVault is your best option. But it would probably make the computer grind for a day or two if you were to try that to a complete TOSEC.