The current presentation of “bonus flat damage” is inconsistent between skills and weapons, meaning that it is not immediately obvious whether the value shown in the game’s UI is before or after % damage multipliers have been taken into account or not.
A player who has not visited either the wiki or GrimTools could be forgiven for not knowing when they are being shown bonus damage with multipliers already factored-in or when they have not.
Some examples
Edit: Yes, I’m red/green colourblind and so I run the game with the colourblindness setting enabled, which is why colours might look odd to the normally-sighted. Thankyou very much Crate for this feature 
Skills: Shown after % modifiers
Here’s a screenshot from the in-game UI. It shows that Dual Blades is granting me +988 piercing damage. It’s not clear from that UI whether this is before or after my % piercing damage is factored in or not. With a trip to the GD Wiki or GrimTools I can see that actually it’s granting me +76 damage and that my % piercing damage bonus is what makes it 988.
Indeed,this second screenshot shows that the bonus damage is inflated to 1045, and all I have done between the first and second is to activate a passive/toggle ability on my weapon (vicious spikes for +75% piece damage).
Incidentally, without using an external resource like the wiki or GT, that’s one of only two ways that I can think a player might just notice that the bonus damage listed for skills is after-percentage-modification. That is - that the displayed damage changes after changing the % modifier. The other way being to manually add up all of the listed damage and try multiplying it by appropriate % damage modifiers, to realise it’s wildly different to the listed damage in character info panel 2.
Devotions: Shown after % modifiers
Devotions work the same as skills. When you get bonus damage, your % bonus damage has already been factored-into the number shown to you. Here’s a screenshot from Blades of Nadaan showing 104 bonus piercing damage. A trip to GrimTools (incidentally, the wiki is out of date for this) shows that it’s really 8 bonus damage, and that 104 is displayed because of my % modifier.
Weapons: Shown before % modifiers
Here’s where the UI goes a little southward. When viewing the stats of weapons (even weapons which are equipped), they show both their base damage and any bonus damage before % modifiers are factored-in.
Here I’ve got some puncturing dermapteran slicers which are showing 54-81 base damage, and 23-34 bonus damage. Again, off to GT and I can see that these are the base values, and have yet to be multiplied up by my % modifiers.
Why I think this should be improved
Whilst I have now learned this, it took me a while to notice and then figure it out, I’m not sure all players (especially those who haven’t visited the forums or dived deeper into the game) would realise that’s how it works. There are no cues in the UI that this is the case and it’s not intuitive. It’s especially troublesome because of the inconsistency between skills/devotions on one hand, and items on the other.
Suggested fixes
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At the simplest level, some kind of visual cue in the UI for skills & devotions would do the trick. A single line in skill mouseover tips would be sufficient. It might read something like Bonus damage takes % modifiers into account. This could be displayed in the subtle grey style at the bottom, like the tip telling the user that they can hold Ctrl to hide an item mouseover tip.
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Another “simple” solution which would work would be to add to the text in the mouse-over tip in the character info panel(s) related to +% damages. A sentence such as this would do the trick: Bonus damage displayed in skills & devotions includes this modifier; damage displayed for items does not. That way, if a player goes looking at their +% damage modifier, they stand a good chance of finding out how the other parts of the UI work.
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A slightly more posh solution would be to add the UI cue to each place where a skill/devotion displays bonus damage. So rather than reading 988 piercing damage, for dual blades it might read 988 piercing damage (including current +% damage).
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Going even further, the game could display both the base and modified damage, although this might be going too far, and over-crowding the tip panel. In that case though, the dual blades tip might read 76 piercing damage (988 including current +% damage). If this were implemented, perhaps it should be toggled via a player options/configuration setting, allowing players to decide how they would like it displayed.