1) The cabinet seems very bass heavy, possibly something Line 6 can fix with a future firmware update, right out of the box I turned on the global bass cut on the back of the cabinet, everything sounded much better at that point, it cuts the bass by 80hz or something to that effect.
I think this is dependent on a number of factors. I have in some cases had many presets come off way to bright. There are so many variables at play. If I go from my SG to my Tele w/fralin p-90's there is a drastic change in tonality. This isn't one amp. It's many balled into one with a great variety of options. I imagine if your amp is on the floor and on carpet, that could also be a big factor. I don't necessarily think from my experience thus far there needs to be any changes (other than the slow start up time, lol)
2) Output of the Flat preset seems to be fairly quiet compared to loaded IR's, go into the settings whether on the interface of the plus or via the powercab edit app and increase the level of the Flat preset to it's maximum +6.0db, again maybe this is something Line 6 can address via a firmware update as this setting seems comparatively quiet compared to the loaded IR's which all have their levels cut by something like 14.0db and when increased this thing get's pretty loud.
My guess is that is a safety precaution because the flat setting is used for your own IR's housed on your modeler. The idea is that program will allow you to scroll through your presets on your device with cab emulation or IRs loaded and not having to change the speaker mode.
3) Run the cab at full output and adjust the volume via your modeler, also you may have to adjust the output of your patches to get a desirable volume level, I've been able to run it this way without getting a clipping warning from the input light on the cabinet.
The way line 6 suggests is that you start with your device set all the way up and then adjust your amp volume. IDK which is right honestly, but that has worked for me thus far :)