Nope.
The only thing that does happen with discordance is that primary skill get secondary CD and special get primary CD with minimum of 0.5 seconds from discordance.
Of course the MH% values switch. 150% blast and 200% orb gets swapped to 200% MH blast and 150% MH orb. Weapon damage will stay the same.
However now Multi Attack and Extra Attack work on Special Skill because the special skill is treated like a primary in terms of CD and damage.
The hero points do not get switched over and the specific damage to the skill.
That means 20 orb will still add ×2 (+100%) damage to orb regardless of whether it’s swapped or not in MH%. That’s also why I couldn’t do the 20 chakram hero point and get it to orb because that would have been OP.
For buccaneer set, it will still add damage to Scattershot skill even if the CD and MH% of primary skill gets swapped to Scattershot and same with the hero points.
This applies with bonuses too 
. Hope this explains everything.
Lastly, Skilled Mythic will not work on Special skill on discordance but will still work on Primary Skill as always.
Yeah discordance is as simple as the description allows it to be.