As someone who has hung around Ganondorf and Gerudo fandom for a very long time, I think there is some significance in understanding what sort of people their story and overall portrayal attracts. We will all read a piece of media with a different lens that is formed entirely of our own lived experiences. That being said, I do think it is detrimental to assign themes to a story when they are very clearly not present, especially when it is around themes of imperialism or the way fictional races inspired by real-life colonized and oppressed people are portrayed. The idea around discussing why a lot of LoZ lore is based in conservative themes such as the Divine Right to Rule being something virtuous, that dark-skinned desert dwellers are meant to be viewed as suspicious and strange until proven otherwise (in a world that has fish people and rock people mind you), or that the ruler of the divine kingdom is actually a god in the flesh, is to ask people to challenge their beliefs and personal biases when they are faced with these themes. We live in a world rife with propaganda, and to twist the reading of any text to suit your needs is not the solution, nor will it help people unlearn the biases they have after being fed this propaganda. All's that to say, it is popular fandom theory that Ganondorf is resisting Hyrule's imperialistic rule by challenging its rulers and refusing to bend his knee, but it is fandom theory at the end of the day. It is important, when writing meta, to distinguish between what the source material is saying versus how we interpret it. I know we all love to joke how the average fan can't read, but realistically if the games set out to give Ganondorf an inkling of story that suggested that his intent was based in his people being oppressed and him resisting Hyrule's oppression, that you as the protagonist were meant to feel guilty for killing him, then people at large would have picked it up. In fact, the few lines that Ganondorf spoke in Wind Waker had many fans discussing whether this meant he had done all this in the name of his people and had taken things too far, or that he had reason apart from a selfish desire for power, that he was suffering, or that he was trying to be manipulative to get Link to lower his guard. The point here is that fans do pick up on these things if they are present in the text.
I think it's an interesting exercise to pick up things in the game that should, in theory, be presented as resistance to imperialist rule but the game itself refuses to portray it in that way. For example, I have spoken at length about how much the Show of Fealty scene and its implications are frustrating because, realistically, being sent multiple invitations that went unanswered until a show of force forced Ganondorf into kneeling before the throne should be seen as imperialism at its worst. However, the game portrays this as Ganondorf's manipulation to get closer to the Secret Stone (which is true, it is probably the greater reason why Ganondorf acquiesced), but it does not, at any point, even try to portray Rauru as being oppressive in any way for twisting the arm of the Gerudo this much until he got what he wanted of them. That is why you get wonderful gems from fans such as "Ganondorf is the one with the power in the room because he may be kneeling but he knows that he's being manipulative" etc. Anyways, the reason I wanted to speak at length about this is because I have found many people who write the sort of meta that goes on to portray their favorite media franchise as progressive when it clearly isn't do so because I don't know, maybe there is a wish there that it is progressive? You can watch, read, and play media that isn't progressive in nature and enjoy it while being critical of its problem aspects, like this is the entire point of media analysis as a study. You can acknowledge that Ganondorf is a man whose desires are based in selfish desire as a character while criticizing that the portrayal of such a character is in the context where his people have been marginalized by Hyrule at large and has suffered at the hands of Hyrule's imperialism, where he and his people are based off people of the SWANA region and thus propagates a negative stereotype of people from that part of the world. You can talk about how Ganondorf is a cruel king while being critical of the fact that a man that has been forced to bow and does not want to bow portrays imperialism in a positive light. These conversations are meant to coexist.