Within the UF context, I wouldn't be surprised if much of the Time Lords' technology operated that way. Gryphon did say something at some point about the Doctor being a really firm believer in the converse of Clarke's Law (i.e. the notion that there might be apparently-magical phenomena that even a Time Lord could not unravel by application of scientific method is repugnant to him). However, several of the stories have commented that Gallifreyan tech seems magical, and that much of it was developed very long ago and/or by people who weren't interested in reproducibility (yeah, I'm looking at you, Omega), and they're no longer sure how it works themselves. So maybe they're hooked into the debugger APIs without knowing it.