Sandboxed lua can't assume it has access things like debug libraries or any of the file IO, among other things. Many setups pretty aggressively remove and/or patch libraries and even large parts of the default global table. Assuming a vanilla lua library environment can make a project like this unusable in many places.
Oh, sure. I didn't realize fennel used those libs in the compiled lua output if you don't call to them. I've never run into this problem and again I've written a lot of fennel that is targeting locked down scripting environments. I probably don't use all of its features though so maybe just got lucky so far.