is plink2 suitable as plink_executable?

Hi,
as we all know , plink1.9 will often switch allele(alt and ref according to maf), but plink2 is fine. So is okay to offer plink2 path into the cfg file especially when the gwas result is from plink2?
 
Besides,  if my gwas result is from 10k WGS samples ,do you recommend using this samples' plink data instead of 1KG?

Thank you for your attention