The Superhero Database Classification number, or SHDB Class, is a number that represents the overall 'power' of a character. All traits of a character are used for calculating the Classification.
What it DOESN'T mean
This doesn't mean that a higher class would always beat a lower class character. But the bigger the difference in Class is, the more obvious it is who'll win in a fight.
How is this calculated
( INT^1.3 + (STR*0.5 )^2 + (SPE*0.5)^2 + DUR^1.6 + (POW + (SPS*SPL))^2 + COM^1.8 ) ^ TIER
Super Power Score and Level
Every Super Power has a score (SPS) that is used to calculate the Class. Each Super Power also has 3 levels (SPL). The level is set when connecting that Super Power to a character. The level determines the final score, of the Super Power, being used in the calculation.
Zeldaverse is logical, consistent and has actual lore or timeline. Marioverse just exists and games events somehow happen
Ganondorf is more consistent and more versatile in magic. Bowser is allegendly more versatile, because Mario franchise has 7x more games than whole Zeldaverse but quality > quantity.
Ganondorf is known to be a very intelligent and cunning character, as well as possessing powerful magical abilities. He is also known to be a skilled fighter and possess great stamina. Bowser, on the other hand, is known for being very physically strong and possessing fire abilities, as well as being able to transform into different forms.
However, it is important to remember that Bowser is a more limited character when compared to Ganondorf, as he is mostly known for being a platform game villain, while Ganondorf is a more complex and developed character. Furthermore, Bowser is also known to be a dumber and more impulsive character, while Ganondorf is known to be smart and plan his actions carefully.
Based on the characters' skills and traits, I believe Ganondorf would be the most likely winner in this fight.