It’s explained here why this is like that Secondary Skill Modifiers, also other skills that behave the same are mentioned.
Not really, or at least not fully. Transmuter for Panetti doesn’t convert Proliferation damage of additional projectiles (convertes Proliferation damage to main target though). But except that part of Proliferatiion the whole PRM tree is converted.
Too much coding / engine changes at this point required for that, might be changed in Grim Dawn 2 to not confuse players. Although 
often adds global conversions to items to remedy this when it’s adequate. Most often then not you can get 50% conversion for those and sometimes even 100%.