This warning seems to be occuring when a PDF file uses a large number of unique fonts or font styles. The pdf-parse library assigns each unique font or font style to a slot in a "private use area" (PUA), which is a range of Unicode code points that are reserved for private use. If a PDF file uses more unique fonts or font styles than there are slots in the PUA, this warning is issued.
Unfortunately, it seems there is not much I can do to prevent this warning, because pdf-parse doesn't provide a way to increase the size of the PUA or to suppress this warning.
Deactivating the warning doesn't seem to work either, because the warnings could be coming from a deeper level in the pdf-parse library or its dependencies, which might be using a different instance of console.warn.
Unfortunately I don't have the time to digg deeper into this. Hope you can someday fix it.