Think about potential custom solutions to the 0-position VCF problem in tskit

Opening this issue as a reminder so that I don't forget to look at this at some point. Relevant discussion starts [here](https://github.com/bodkan/slendr/commit/3a8c7a9380e08a8d80ac6ebeae3894dcb92e7cca#commitcomment-153843587). Also keep an eye on [this](https://github.com/tskit-dev/tskit/issues/2838#issuecomment-2729772611) tskit discussion.

@janxkoci