I consider myself a God Card expert and I admit the God Cards abilities can be ambiguous or contradictory. But most of their effects are known from the many appearances of them in the anime and manga. The anime God Cards on YGOPro are extremely close to their anime/manga counterparts. The only differences or remaining ambiguities are:
1. Ra's 'Special Summon' abilities. During Battle City Ra only used his One Turn Kill and God Phoenix abilities when special summoned. Seto's translation of the Ra hieratic text hinted at this being a requirement. However, during the Ceremonial Duel, Marik says that if Yugi used the other effects of Ra (who was Normal Summoned), he could increase Ra's ATK to nearly 15,000. This would have been if he had tributed Slifer and Obelisk + paid all but 1 of his LP to increase Ra's ATK and DEF. In the only episode of GX where Ra appeared, Ra was Normal Summoned and still was able to use his other abilities. So its then left up to interpretation.
2. Trap Cards working on Gods. I can't remember an episode where a Trap Card worked on them, but there might be. It would have to be a non-targeting, non-removing or non-negation Trap. Again, not fully clear. I'm fine with Traps working for 1 turn assuming they don't destroy, target, or remove.
3. Having to be a chosen Duelist to use a God cannot be implemented into the cards, for obvious reasons. Just like we can't force users of Ra to recite the ancient hieratic text.
4. I'm pretty sure God Cards cannot be negated, based on what I know of them. So Skill Drain or other non-targeting negation spells shouldn't work.
5. In the manga only, there was a hierarchy of the God Cards, where Obelisk's and Slifer's abilities didn't work on Ra. This was never mentioned in the anime, but I like the idea. God is the highest of the Gods, representing heaven and earth, and I cannot imagine those underneath him working.
6. There are 3 cards that bypass the immunities of the Gods: anime-Pyramid of Light, anime The Wicked Eraser, and anime Ra's God Phoenix.