What is the technical explanation for why Archive Utility can break certain apps, while other unarchivers won't?
The file attributes are not the data that's stored in files, it's the information stored in the file system. Different archiving utilities may interpret information differently. It's either:
a) File attributes before zipping are incorrect and (some) unzipping utility fixes it
b) Unzipping utility has a bug.
I checked the archive with tar utility (widely used and well know utility). The file "Neuron.app/Contents/MacOS/Neutron" has no "x" attribute in it. The app creator probably forgot to set that attribute, so basically it's cause a).