@thermokarst Thank you very much for pointing that out. I did not know that is not an issue any more.
When reading the code of _demux.py on github, I have the impression that this would still be an issue because on line 367-368 (q2-demux/q2_demux/_demux.py at dev · qiime2/q2-demux · GitHub) a barcode map is already being generated before checking the argument of golay_error_correction (which is on line 387). And when generating the barcode map using the _make_barcode_map function, it will check if variable length of barcode is inputted and raise an error if so. And in that function, the golay_error_correction flag is not an argument. I'll edit this post to remove this paragraph if I am wrong. Sorry if my post would cause any confusions.
And disabling the Golay correction is still not sufficient to solve my problems because as I mentioned, the issue is rooted in the barcode sequence file which includes barcodes shorter than what is in mapping file (most of them are 1 bp short). If qiime demux only allows exact match, those sequences would be discarded which would leave many of my samples with no sequences at all.