Puzzling. I can't say what would cause that. But probably not serious, if I had to guess.
What you need to be on the lookout for (based on my own experience here in mild coastal Baja California) is small bugs at the base of the leaves, which might leave behind "snack marks" where they suck the juices from tender young leaves and the green part of the stem where it is in active growth. Scale insects or mealy bugs. What you've got in terms of damage/discoloration does not really match, but my response to any sort of weird spots on leaves is to look for insects hidden away in the nooks and crannies, in like a forensic way. They like to hide in between the leaves at the base. Easily eliminated once discovered, this would be the main active threat for my Pachypodiums.
One thing I have noticed over various years with various Pachypodiums (and living in a very arid climate much like your own in terms of total rainfall) is that the leaves are often deformed or distorted when plants first put them out. Some plants seem to be in such a hurry some times that the leaves end up a bit gnarly once they're full size. Maybe they're complaining about insufficient water (I tend to underwater) but that's about it. This just as an observation should you come across distorted leaves and wonder if that's anything to worry about.
Three different plants here...
