First off, you don’t look at the wfm, and use that as a guide as to whether or not you are clipping on the way in.
Secondly, I don’t know where this trim so no peaks are greater than -12dBFS comes from…
the small input meter on the transport bar shows red clipping at the top of the bar
Are you talking about the Audio Activity (Default In Ch) to the right of MIDI In Activity? That’s just duplicating the input fader - which is really what you should be looking at.
Guitar’s going into a Focusrite Voicemaster Pro in order to use some light compression to tame peaks, then into a Focusrite Scarlett 2i4 which is my audio interface/preamp.
Typically, you go into the mic pre first, and then a compressor if you want and/or need to. I am not familiar with either of your two pieces of gear - is it not possible to go guitar > mic pre > comp > soundcard? That’s really what you want to do.
Yes, you want to try and avoid clipping. However, that’s not to say that if you see any red, that it’s all bad. Some may be ok - some. You definitely want to avoid constant red, but if you see a touch here and there, you are probably ok. I am not telling you to definitely go into the red, however. Red does not necessarily mean clipping. Red is a warning. Take it as such.
Again, I am not familiar with your gear, but do either have meters? Let’s assume so. You want your level to be as hot as possible (there are occasions you don’t, but generally you do), meaning that both pieces should have a good level. Again, going into the red a bit is most likely ok. If you see too much red, back off a bit. Next, you may want to have a look at the sound card’s control panel (sw) as there are probably adjustments there. Depending on how the driver was written, what you are seeing is pre-Cubase. Or at least, that is what you should be seeing. Next, you want to adjust the input fader in Cubase so that it too has a good, strong level, without too much (if any) clipping. If the meter goes up into the red (past 0) too much, back off.
That’s about it. Have fun.