A wiretap warrant involves government access to a public/regulated utility. A software warrant involves government access to a private residence. The former is a matter of "hi, we're the government, we have a warrant to tap line XYZ"; the latter is a matter of "let's sneak this into a citizen's private effects, on their private property, with only us in the know". And by "doesn't have root", I mean it can't create whatever false forensic trail you want within said citizen's private effects. If you insert your tap/backdoor/soldier in the middle, it can pretend to be one or the other or even both, but (1) if Ada and Bob are using proper encryption it can't fool both and might not fool either, and (2) encryption or no encryption, if a third party - e.g. a technical expert for the defence - audits Ada's and Bob's machines they'll figure out something fishy is going on. If you've got root on either person's machine, however, you can plant incriminating evidence that can be a lot harder or even impossible to show as fake no matter how good the defence's technical experts are, especially if you're a state actor with a state's resources to get the job done.
"More to the point, where you attach a tap has nothing to do with quartering soldiers in time of peace or war."
I do realise the Third isn't applicable for a number of technical legal reasons (and despite them all I'd argue it should be, but good luck with that, self) but please consider as a rhetorical exercise: /what/ is a soldier, and /why/ is it unconstitutional to quarter a soldier in any house?