When profiling guitar pickups you might want to connect Bode Plot to your guitar processor. That kind of test makes a perfect sense, as it allows you to profile the whole signal chain including guitar pickups, internal load, cable - physical or virtual, if using wireless system and the guitar processor input impedance.
The good news is all of the above is possible, as most guitar processors provide a USB interface and technically are audio interfaces.
However you should be aware of several caveats.
First and foremost, the guitar processor is an audio interface with direct monitor turned on by default and oftentimes this direct monitoring may not be turned off at all. Indeed, it's a device designed to operate autonomously, and whatever tools it has for interfacing with a computer, are just convenience/extra value features. In practice that means you might be forced to look for creative ways to get rid of the positive feedback.
Usually the workaround is as follows:
1. Select an empty preset, where input is not connected to the output, effectively breaking the feedback loop
2. Collect the input signal from a USB input dedicated to sending dry unprocessed signal - most guitar processors allow to record the unprocessed input for re-amping.
Configuring Fractal Audio FM3 as Bode Plot audio interface
The second problem you might have to deal with is an "intelligent" input impedance handling by some advanced processors, like Fractal Audio FM9 and Axe-FX III. These processors may exhibit noticeable live parameter adjustments of input signal chain while adapting to an input source. This tweaking results in abrupt changes of volume happening when connecting a guitar or bass with active preamp during lasting for the first several seconds. As a result the frequency response plot captured through such processors might exhibit extreme fluctuations spanning first measurement points. You might have to disable the auto input impedance mode when using these devices with Bode Plot.