The error is caused by the second step in precompile, at the first line of the openContext function. When passing the AST through the parsedModules optional argument in openContext, the openContext function drops the sources computed in the first step of precompile (which contain the stdlib declarations):

const modules = parsedModules ?? parseModules(sources, parser);

This causes missing reference errors in resolveDescriptors later.

It seems to me that instead of dropping sources, the function openContext should take the union of sources plus the optional argument parsedModules. Like this:

const parsedSources = parseModules(sources, parser);
const modules = typeof parsedModules === "undefined" ? parsedSources : [...parsedSources, ...parsedModules];