My friend is using plink 1.9, this is a simplified version of what I am reading from someones elses' code

He first reads in a vcf, split pseudoatuosomal regions

plink \
--vcf file.vcf \ 
--double-id \
--keep-allele-order \
--make-bed \
--split-x hg19 \
--out outname \

zeroes heterozygous haploid calls

plink 
--bfile outname \
--keep-allele-order \
--make-bed \
--set-hh-missing \
--out outname_hh_fixed

Merges the PAR back in

plink \
--bfile outname_hh_fixed \
--merge-x \
--make-bed \
--out outname_hh_fixed_merged

Converts the PLINK to VCF

plink \
--bfile outname_hh_fixed_merged \
--keep-allele-order \
--recode vcf-iid \
--real-ref-alleles \
--a2-allele vcfinfo.txt 4 3 0 \
--out final_vcf.vcf

If I understand --keep-allele-order prevents plink from flipping around alleles and preserves the REF allele in the original VCF as A2 (major allele in plink)

I have two questions:

1. Why is --keep-allele-order not needed when merging PAR back in?
2. Why does PLINK need you specify --keep-allele-order and --a2-allele when writing the VCF in the last step? I think I understand from the documentation that column 4 of vcfinfo.txt will be used as a guide for setting alleles in that column to A2 (or REF in the final_vcf). I am just kind of stumped as to why you would need to supply a column of alleles to designate as A2 if we are already saying --keep-allele-order. Wouldn't the correct order already be baked into the .bim file then? Thank you.