Yes, they do.

I'm considering switching the way I make the VCF.  Mutect2 v4 now has an option to emit germline sites.  So, I can redo my pipeline and rerun Mutect2 on all the samples, and I should end up with a more reliable VCF file, and more consistent one.

In the meantime, I'm just going to set the QUAL field to ".".  The MBQ I had already removed from the somatic calls.

Looking at your code for filtering, I would think it wouldn't be hard to account for "." in fields, like this perhaps:

.filterVcfByBQ = function (vcf, tumor.id.in.vcf, min.base.quality) 
{
    n.vcf.before.filter <- nrow(vcf)
    idx <- numeric()
    if (!is.null(geno(vcf)$BQ)) {
        idx <- which(as.numeric(geno(vcf)$BQ[, tumor.id.in.vcf]) >= min.base.quality)
    }
    if (!is.null(geno(vcf)$MBQ)) {
        idxT <- which(as.numeric(geno(vcf)$MBQ[, tumor.id.in.vcf]) >= min.base.quality)
        idx <- union(idx, idxT)
    }
    if (!is.null(rowRanges(vcf)$QUAL)) {
        idxT <- which(as.numeric(rowRanges(vcf)$QUAL) >= min.base.quality)
        idx <- union(idx, idxT)
    }
    if (length(idx)) 
        vcf <- vcf[idx]
    flog.info("Removing %i low quality variants with BQ < %i.", 
        n.vcf.before.filter - nrow(vcf), min.base.quality)
    vcf
}

Or, if you want to make sure you use only one of the three for any one variant:

.filterVcfByBQ = function (vcf, tumor.id.in.vcf, min.base.quality) 
{
    n.vcf.before.filter <- nrow(vcf)
    idx <- numeric()
    idxTested <- numeric()
    if (!is.null(geno(vcf)$BQ)) {
        BQ <- as.numeric(geno(vcf)$BQ[, tumor.id.in.vcf])
        idx <- which(BQ >= min.base.quality)
        idxTested <- which(!is.na(BQ))
    }
    if (!is.null(geno(vcf)$MBQ)) {
        MBQ <- as.numeric(geno(vcf)$MBQ[, tumor.id.in.vcf])
        idxT <- setdiff(which(MBQ >= min.base.quality), idxTested)
        idx <- union(idx, idxT)
        idxTested <- union(idxTested, which(!is.na(MBQ)))
    }
    if (!is.null(rowRanges(vcf)$QUAL)) {
        QUAL <- as.numeric(rowRanges(vcf)$QUAL)
        idxT <- setdiff(which(QUAL >= min.base.quality), idxTested)
        idx <- union(idx, idxT)
    }
    if (length(idx)) 
        vcf <- vcf[idx]
    flog.info("Removing %i low quality variants with BQ < %i.", 
        n.vcf.before.filter - nrow(vcf), min.base.quality)
    vcf
}

These assume "." is translated to NA.