I will refer to two posts (links below), whereby similar question had been asked in the past: "How to extract normalized counts with covariates in the design" and there was no direct way to get the desired output.
Later on it was suggested to use removeBatch (https://support.bioconductor.org/p/62954/)
I have used SVA to account for not only batch affects but also other possible hidden covariates. In the current manual: https://bioconductor.org/packages/release/bioc/manuals/DESeq2/man/DESeq2.pdf
plotCount functions has parameter "returnData". Is this the correct parameter to be used to extract the "custom post-normalization counts" and save to a file?