Its probably skipped for brevity.
In episode 97 of season 2, Bakura offers three monsters as a tribute to summon the Winged Dragon of Ra, just like any other monster he instantly appears. Sphere Mode, as well as the cinematic appearance of the summoning, was probably just skipped because after Joyful Doom's effect a Ra with 0 ATK is not a spectacular sight ...
A bit of context:
A short while before that duel, Kaiba had woken up from his coma induced by Yugi (Yugi had broken Kaiba's mind at the end of the "Exodia game". Yugi had told Kaiba to reconstruct the puzzle of his mind, to remind himself of what was important to him).
When Kaiba succeeded in reconstructing the puzzle of his mind, he realized that his ...
The 5D's is meant to represent the legendary 5 Dragons (Signer Dragons) that the protagonists (Signers) use in order to fight the antagonists (Dark Signers).
These dragons are:
Red Dragon Archfiend
Black Rose Dragon
Ancient Fairy Dragon
I honestly can't recall any where he didn't have an 'additional' affect to something, or went and did something impossible for a card game (like smashing the moon against mako or breaking the float ring against the floating castle)...
Also pot of greed lets you draw 2 cards from your deck