How should the SAM MD tag match the CIGAR string?
The MD string doesn't apply to soft or hard clipped regions,. so your example read becomes 43G42. Since variant calling using something simplistic like this is only ever going to use the aligned portion, I guess there was never much reason to bother with adding in soft-clipping information. This also means that you need to parse the CIGAR string if you're using the MD string.