I’m not sure the instrument level inputs on the focusrite interfaces are particularly well thought out or implemented - if you can take care of your first stage of clipping before you get to the interface (i.e., stick a pedal infront) I think you might get better results. Otherwise a fet-based di like a countryman 85 will also be good.
I think problems arise because the dynamic swing between your most powerful output (usually a muted E powerchord but maybe a pinch harmonic beats that), your sort of middle volume regular playing and your quietest playing is so great that there’s just no way to set up the interface and the amp sim that you get good results across the whole range. Better to compress your signal first in some way whether that’s a clean boost, light drive, compressor whatever.
Even even better in my view is something like the AMT legends series preamp pedals - run the guitar into that, let your main tone generation be done in the analog world and then run your cabinet and room IRs in the DAW along with whatever post effects you fancy.
If you do want to stay purely in the box you could try ensuring that even the highest level out of the guitar doesn’t clip the interface then use a gain plugin (like Utility in Ableton) to make up the gain before reaching the amp sim.