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 and would cost precious animation time they could use to explain what Pot of Greed does for the hundredths time (however I couldn't find the Japanese original to check if it's missing there too).
Shown on screen or not, Bakura and Marik's Soul both were capable of summoning the Winged Dragon because of their ancient Egypt heritage and Marik's knowledge of the card's text (both are additional requirements in the Yu-Gi-Oh Universe, although in GX! an Yu-Gi imposter manages to summon Ra despite that).
As far as I remember in later episodes the chanting and sphere mode were also skipped some times, probably to get more story into the limited time of an episode.
In-Universe the explanation could be similar, since Ra was summoned with no ATK, the Duel Disk Device could have seen Sphere Mode as not necessary although one can only guess or maybe it was enough that Marik (or his Soul) already successfully summoned Ra once and proved worthy to control him. Also the God Cards seem to be special in the way that they seem to have a will on their own, which is indicated in several episodes and maybe Ra didn't feel like it.
One should note that Winged Dragon of Ra wasn't an actual playable card at that time and had no official effects and writers often bended or completely changed the rules of the game or single cards to fit the narrative. Only much later the Winged Dragon of Ra got an official effect and an actual Sphere Mode as well as the dreaded Phoenix Mode. And even in the Manga cards have different effects than in the actual TCG although the God Card's effects were more defined in the original Manga.