MANE/MANE Select is an annotation and I've found that retaining more annotations and filtering them downstream is a more sustainable/long-term solution than asking the annotator to remove records at output time.

I personally use bcftools +split-vep | awk to filter VEP output. Along with the ability to select only records where MANE=1/YES/whatever_the_positive_indicator_is, you can use options such as -s worst to pick the worst consequence per variant, which is often on the MANE transcript. There's also the vep_filter tool from EnsEMBL.