It's not just you. I see the clip light go red on the top path with a number of factory presets. With that said, I don't really hear digital clipping when that happens. I'm almost always using both paths so I suspect that the final output stage is what's most important and I don't see that flash red very often.
Beyond that, I find the factory presets in Stadium to be quite a bit louder than those of the original Helix. After sound engineer feedback, I tended to run my presets on the more quiet side with my old Helix which often had amp "level" (the final level control in HX systems) around 5'ish depending on the amp. In the new Stadium Agora amps, with their new level control that looks more like an audio fader starting a 0 and then boosting or cutting, I often have to make significant cuts to achieve the same output levels. For example, for a Matchless with a level of 5 in old Helix, I have to cut the new Agora AC30 to -21 db. It seems weird but still works fine.
I recommend using some kind of outside metering to determine levels. I use the Youlean Loudness Meter most of the time as it's a simple stand alone app. Other times I have used an analyzer tool in my DAW (Logic). I tend to run my presets between minus 18 and minus 10 LUFS (loudness units). That seems to always leave headroom and the engineers seem to appreciate it. I also run the outputs at Mic level, not Line.
In terms of gain staging, it's a good general principle to shoot for unity gain across all your amps and effects. Turn everything off and see what your direct guitar is like gain wise. Then I shoot for keeping most of my amps and effects around that same level. The exception is the gain pedals. In my view, gain pedals are meant give you more color to the sound AND boost the output a bit. I know others might not want that but that's how I do it. I set each gain stage to go up by around 2 LUFS. Another exception is that sometimes I will raise the "Mix" on a reverb or delay on a snapshot. That definitely raises gain at the same time but that's usually for a more dynamic section of a song so it helps compensate for pulling back.
For a while, I used to put the LA2A compressor model at the end of my whole change (LA Studio Comp). I would set it for 2-3db of compression at my loudest sound and unity gain for clean. That can help smooth out gain changes and help "glue" things together as the engineers say. Over time I stopped as it took too much adjustment for every sound and song because it reacts differently with how much gain you feed it. Also, most engineers are compressing it at front of house as well as things can get too squished if you're not careful.
So my recommendation is use some kind of outside metering, decide on a target level, and then adjust everything to fit that standard. If you use one preset for a whole show then you're done. If you use one song per preset, then you have to level all your presets to around the same levels for a cohesive set.
Hope that helps!