Gather around kids, papa V has a story to tell.
To understand the way Ra works in the show, we need to point out a few important things about the divine beasts. We all know that Pegasus created the Duel Monster cards based on stone tablets he found in ancient Egypt. Unknowingly, Pegasus recreated the ritual battles that magicians and kings used to solve their conflicts, and turned it into a game of cards. It is noted throughout each arc of the series that the duel monster spirits reside inside the cards. Slifer (or Osiris in jap version), Ra and Obelisk where LITERAL Egyptian gods and these deities where being forced into the world by people who where trying to design cards based on them. Soo against the gods will, these people unknowingly where creating a vessel for the gods's spirit which they would now be bound to reside in. Needles to say, everyone who worked on designing the cards was either hurt or killed. Pegasus was also going to suffer the same fate but he survived the wrath of the gods only because he was shielded by the magic of his millennium eye. Some people couldn't understand why Pegasus regretted creating the cards, but couldn't tear and destroy them.
These people easily forget the part where the spirits (in this case gods) where directly connected to the cards. Destroying them would mean that you are assaulting an actual deity and you risk bringing the wrath of the gods upon yourself. Soo Pegasus decided to seal them away. The cards have a will of their own. Especially the god cards.
Soo let's talk about the strongest god card (At least in the anime), The Winged Dragon Of Ra. The first time Ra was shown being played, was when Odion used a fake version of the card. Keep in mind that the spirit of the real Ra, reside in the original card that was withing Maryk and it was livid with anger when it was summoned trough a fake card. Which is why we don't see Ra clearly when it appeared in that duel.It was being disrespected by being forced on the field trough another vessel. The wrath of Ra struck both Odion and Joey with lightning and then the divine beast disappeared from the field. Odion and Joey survived, however the same cannot be said for the people who previously tried to use a fake card of Ra. It is shown in a flashback that whenever one of the minions of Maryk tried to summon Ra trough a fake card, the divine beast would struck and kill the person who dares to do so. (I guess the show really wanted to teach people that playing with fake cards is not ok XD )
Now let's talk what happens when you play the real card. May Valentine managed to summon the winged dragon of Ra and she was not hurt when she did so. However, the god sensed that she was a nobody with no royal heritage, and so it came on the field in a sealed state in the form of a sphere. Ra wanted to test if she was worthy to control it's power by forcing her to speak the ancient chant written on the card. She couldn't, which is why even tho Ra was on May's side of the field, control of the monster switched to Maryk who knew how to read the ancient text. Meaning that only those who prove themselves worthy, could use the power of a god.
Later on in the series, Maryk summoned Ra multiple times throughout the series, without the need to read the ancient chant. However in the final face off against Atem, when Maryk summoned the winged dragon of Ra for the last time before the game ended, Ra once again appeared in the sealed sphere mode, even tho Maryk played Ra 2 times before that during the same duel and he didn't need to say the chant up until this point. This is a perfect example of how the divine beast has a mind of it's own and it will test it's owner to know if he is still worthy to wield it's power. What I realized right then and there was, that reading the chant is not only necessary to prove if you are worthy to wield the power of the strongest god card, but also a way to show your respect to the god.
Now let's finally move on to the duel with Yami Maryk and Yami Bakura.
Yami Bakura was in control during the duel and his aura was not that of a mere mortal. It is possible that Ra sensed this and deemed unnecessary to test Bakura. It is also worth noting that the soul of Maryk's good side was also there inside Bakura. Soo even if Ra did decide to test Bakura, the good side of Maryk would've helped with the reading of the chant.
It is worth mentioning for those who didn't knew, that the chant in the dub and the chant in the sub sound completely different. And it's not because in dub they speak english and in sub they speak japanese. In the dub Maryk says the whole "Great beast of the sky,please hear my cry" to unleash Ra from his Sphere mode,however in the sub version, Maryk literally mumbles words that no one could understand. The many effects of Ra are hidden inside the text of the chant. Which is why when Maryk uses the point to point transfer ability and instant attack, in the sub version he mumbles a part of the ancient chant because the effect is hidden within it. While in the Dub version, Yami Maryk simple says what effects he is going to use. The good Maryk knew how to read the chant, but he was obviously not smart enough to figure out the hidden effects in it. Which is why the good side of Maryk was soo surprised when he learned that Ra had more abilities. Yami Maryk had all of the time he needed while he was sealed in the subconscious of his good counterpart, to figure out the effects in the chant. He also slowly but surely was manipulating the mind of his good counterpart, distracting him with feelings of hate, thoughts of revenge and desire for power.
In Yu-Gi-Oh!GX, Industrial illusions created a new copy of the winged dragon of ra, since once Atem went to the afterlife, he took the original god cards with him. It is not explained if there where any incidents during the process of the creation of the card, but the company wanted to recreate the card for testing purposes. The card was very much original and it served as a new vessel for the spirit of the Winged Dragon of Ra.
Franz, who was a card designer working for Industrial Illusion, stole the copy of the winged dragon of ra. He was able to create the only card capable of binding an Egyptian God against its will, "Mound of the Bound Creator". Which explains why Ra never came on the field in it's sphere mode. Franz could also use all of the ablities of Ra without chanting the anchient text. Due to being bound against it's will and unable to retaliate, Jaden could sense the sadness coming out from the card. Later in the same duel, Jaden summoned the winged dragon of Ra on his field to defeat Franz. Wether it was because Jaden was the reincarnation of the supreme king or because Ra wanted revenge on Franz, Ra allowed Jaden to use it's power, without the need to speak the ancient chant.
Anyway, I hope this comment was helpful and eyeopening.
P.S. Sorry for the long explanation. I felt that everything I mention was important and connected. Also I apologize if I made any grammar mistakes. I hope you found this explanation useful.