Regulation of the replication of mtDNA at embryonic level
This is a topic which seems to be not very clear yet. References say that this is obviously dependent on the tissue and the "gene dosage" seems to play a role, and that this is probably regulated by a yet unknown factor (see "Mitochondrial DNA replication: what we know." and "Replication and transcription of mammalian mitochondrial DNA.").
Newer articles suggest that it depends also on the transcription of the mtDNA (see "The interface of transcription and DNA replication in the mitochondria." and "Mitochondrial transcription factor A regulates mitochondrial transcription initiation, DNA packaging, and genome copy number."). I will see, if there are other interesting publications, if there are problems with accessing these articles, let me know.