What does it mean to "directly" modify?

What are some examples of cards(quickplay Spells) that do this, and some that don't?

Rush Recklessly
Blast With Chain(trap)
Rare Metalmorph
Metalmorph

Is Graceful Dice's boost considered "directly" modifying?

Things like...

Rush Recklessly
Rising Energy
Limiter Removal
Metalmorph
Rare Metalmorph
Shadow Spell
Mask of Weakness
Shrink
Blast with Chain
The Big March of Animals
Pyramid Energy
Graceful Dice
Skull Dice
Deal of Phantom
The Reliable Guardian
Mirror Wall
Fairy Box
Energy Drain
Bark of Dark Ruler
Aqua Chorus
Covering Fire
Reinforcements
Castle Walls
Miracle Kids
etc


Reverse Trap does NOT "directly" modify a monster's ATK and DEF, but rather the increase/decrease given by an effect already doing the modifying (hence, why it can't be used in the Damage Step).