Given the extent, some of the heteroplasmic SNPs should be genuine (see comment above on the used polymerase). When looking at the supplement tables reporting the haplotypes exemplifying the heteroplasmy, one thing strikes the eye: they are all satellite haplotypes of the reference plastome sequence.

If common biparental inheritance would be the cause of the heteroplasmy, one would expect some...

The standard-used Taq DNA polymerase is not a proof-reading polymerase and prone to replication errors (long known among those who cloned a lot, hence, we changed to proofreading polymerases quite some time ago) It even says so on Wikipedia: "One of Taq's drawbacks is its lack of 3' to 5' exonuclease proofreading activity[4] resulting in relatively low replication fidelity" with reference to the...