There is no real canon.
The manga and things like DSoD & even S0 are separate canons.
Future shows like Zexal and Arc-V are separate canons, and their mangas are separate canons.
There is no official timeline, so just take each series for what you want out of it.
The different continuities presented in the manga and anime it's been around since gx.
However in the original yu-gi-oh! The manga was written by Kazuki Takahashi himself. As well as the plot of DSoD as continuation of the original manga.
DM anime is just and censored adaptation of Takahashi's manga and by censored I mean the Japanese version as well.
Quite frankly I don't think it matters if they change names of characters. They change names in all countries for a ton of shows this isn't something unique to 4Kids.
Anoymous
