Is there any reason for the variation in mitochondrial DNA size?
One of the contributing factors the size of the yeast mitochondrial genome are 'selfish' mobile genetic elements termed homing endonucleases genes (HEGs).  These genes are typically found in introns that encode site-specific DNA endonucleases.  These endnoclueases cleave the HEG- alleles during yeast mating leading to DNA recombination using the HEG+ allele as template.  I suspect over time as organisms became more complex and HEGs become unable to mobilize they would become fixed in the organisms genome.  Upon being fixed there is no selection pressure to maintain the open reading frame of the HEG or the intron its encoded within (ref).  This causes the eventual loss of the HEG and intron since they provide no real benefit to the organisms genome.

I don't know how much of the yeast mitochondrial genome is taken up by these introns.  I believe that there are 4 of them in yeast some of the introns also require reverse transcriptase for splicing and mobility.  Other fungal species can have many more introns and sometimes weird things like introns embedded within introns.