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That's just the base Damage - the end game of TL2 depends heavily on the Strength_Dps and Focus_Level multipliers plus some decent Critical Chances.
Verbose Damage Settings can be selected within the game Options to see all Damage Events.
There is no yes or no answer to your question: weapon-based skills are not universally worst than flat-damage skills, and flat-damage skills are not universally worst than weapon-based skills.
You mention some skills do only 50% of weapon DPS, but Strength counts into that, and also Focus if the skill deals this "50% of weapon DPS" as say Fire damage
However the Elemental Damage of Weapons adds to the total Dps a Dps Skill will use hence both Strength and Focus are beneficial. The issue is that vanilla game weapons don't usually carry high amount of Elemental Damage with few Legendary exceptions.
Elemental Skills sometimes deal Dps as (Any Type) Damage which is using both Strength and Focus.
Some Skills are exclusively dependent on Focus and Level which list Damage around 10,000 however this is not better or worse than Strength if factoring Critical Strikes and other factors.
Ultimately it's best to just build around the Damage System of a Class or specific Skills.