@RC: Ah, no didn't see the edit.
And sure, space magic can handwave a lot of problems away. However, what you say about the fleshwrapper is not entirely true. Sure, cosmetic changes or simple changes are simple with it, but actually creating something with it is hard.
See the following
http://www.bay12forums.com/smf/index.php?topic=136149.msg5334056#msg5334056 and
http://www.bay12forums.com/smf/index.php?topic=136149.msg5337843#msg5337843 (they also exist as citations in the organochemistry overrider page. Glad I made those questions to piecewise, they gave me some ideas for Hephaestus research.)
Machines are more than software. That's what I'm talking about.
For an extreme example, think of some kind of clockwork robot. The only way to alter that robot would be to alter it physically. For something more likely to come up, imagine having to change the position of a physical object, perhaps to reestablish a physical connection or to change the resistance of a resistor to melt a component. Just like the Overrider gives you the opportunity to mess with the DNA of something, you'd also get the chance to mess with the internals of the machine. Hard to do but potentially very useful. Don't know, if piecewise thinks it's too OP or open to abuse he can stick to software.
@Nik: See the links I gave RC. The reason that works is because you're just altering their body, not controlling them. You're just changing their DNA or healing a wound or stopping their heart.
Why would you control computers with it? It's just a "
join the dark side create lightning" amp not an "understand machines" amp. Again, look at the posts above, that would require at least some understanding of what you are trying to do, a way to understand it, a way to get inputs and outputs... Much more complex than create lightning.