1) Does the cheats file provided here contains the extra stuff from the Additional Cheats mod, and the feature for disabling save file flagging?
It contains a special version of Additional Cheats designed for Expanded Arsenal Mod, which replaces all regular weapon cheats with Expanded Arsenal Mod ones and enables SilverLink cheats (I've also removed No Glitches cheat as you can toggle glitch effects via Sandbox+). They all have flagging disabled so don't worry.
2) If I want to start a new game of play the DLC missions, is there a way to disable the Character Behaviour and Spawn part of the mod only (like, temporaly moving specific files away from the game folder), or do I need to completely uninstall, verify files, play, and then install again?
Like I said on the previous page, I've been planning to create an optional no NPC Behaviour patch for a while but it's one of the fundamental mods so I don't think it would make sense. Although you can complete How the Saints Saved Christmas missions with just
Expanded Arsenal Mod - this way you won't lose any weapons, upgrades nor unlockables included in the mod. Simply use the uninstaller provided in the archive (no need to verify the cache, modified VPP_PC files won't break anything), install Expanded Arsenal Mod, complete the DLC and reinstall the pack.
3) Is there a way to edit the
Reasonable Body Slider Mod to make it only alter body shape, but no facial features?
Probably there is, but I've never messed with body sliders so I can't help you with that.
4) I guess the Dark Rain mod is totally incompatible, right?
There shouldn't be a problem in using its weather files, honestly. Go ahead and try to paste 'rain.xtbl' and 'weather.xtbl'. Just make sure not to replace 'character.xtbl' and 'preload_anim.vpp_pc', these files will break the pack. Also, I'd recommend you to delete 'default_district.xtbl' and 'skybox_effects.xtbl' files, as they come from shitface's weather mod and might collide with Dark Rain.
Keep in mind that you're doing all this stuff at your own risk, don't ask me if it actually doesn't work properly.
5) Do I need to always run the game using the custom launcher, o can I run it once, configure my settings and then ignore it?
Nah, the launcher is completely optional (although recommended for changing the settings, as it contains many options which aren't available in the graphics menu; it also sets 'display.ini' to read-only so the game cannot change your configuration).
Anyway, I'm glad you eventually got it working. Have fun!