What does it mean "During End Phase target RDA in GY...."
Is it optional?
Because previously it said "Once per turn, you can target one opponent monster, negate its effect..."
Those are two different effects. The "during the end phase" effect is mandatory, and will activate even if you don't activate the "once per turn" effect.
You can flip it face-down to prevent it from returning to the extra deck, but on the turn it is flipped face-up again, the effect will activate during the end phase of that turn.
It's not mentioned on Majestic Red Dragon's ruling, however, Majestic Star Dragon which has a practically identical last effect, has an official ruling stating that the effect still activates even if the Stardust Dragon is not in the Graveyard. In that case, Majestic Star is still forced to return to the extra deck, but no Stardust Dragon is summoned.
Apparently, for Majestic Star Dragon's case, it can be used with Wicked Rebirth, as WR only negates' the monster effect while it is on the field.
Hence, allowing you to keep it on the field but still can use its tribute-negate-nuke effect.
As you said, the real issue is how to properly summon MSD (easily) and send it to GY before it can be revived by WR.