The AO sprites are semi-transparent, with the black somehow representing transparency. I can't remember quite how it worked, but I do remember running into issues with the middle of sprites randomly being see-through when I last played around with them. I think I rendered them properly once with a DX blend mode, but I can't remember what it was.
If you want to be really clever and actually make this flexible you really need to implement some kind of scripting. I'm currently working on a VM-turned-script-interpreter (that still reads from an intermediate bytecode-like format) and one of my first ideas for when it's done is actually a bit like this, or at least something simpler which starts to define a framework for an ALIVE-like engine. My end goal would be total asset replacement, though, to allow for things like hats and colour customisation a-la Aji's Oddworld dream.
ALIVE has lots of little intricacies. You really need to think carefully before you dive too far into this. Really carefully.
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