Short answer, loadman (the dev supporting mala now) doesn't have tons of free time, and support for transparent pngs doesn't come easily out of the box with Delphi, which is what Mala is written in, so it just hasn't risen high enough in priority to allocate time to it.
Mala's not open source because of a request from the original author, as I understand it, not because of any decision by Loadman. Further, Mala uses a few proprietary libs that require purchase, which makes opensourcing it onerous at best.
I agree it'd by nice to have the alpha channel trans support that PNGs offer, but, what's there is what's there for the time being.
I hope to include trans PNG support via my Mala addin Engine18. But, I'm in the same boat, in terms of time, right now.
Do you have any specific requirements? That might help me narrow the task down a bit...