Control Undead is not a "Turn" effect
Strictly speaking, the Control Undead feature isn't the same as "Turn Undead". Other features that turn undead (or other creature types) are pretty explicit about what they do. Take the Devotion Paladin's Channel Divinity, Turn the Unholy, as an example:
As an action, you present your holy symbol and speak a prayer censuring fiends and undead, using your Channel Divinity. Each fiend or undead that can see or hear you within 30 feet of you must make a Wisdom saving throw. If the creature fails its saving throw, it is turned for 1 minute or until it takes damage.
A turned creature must spend its turns...
Emphasis mine. The feature as written for Clerics is also identically written.
By contrast, the Control Undead feature makes no reference to "Turning" the Undead it affects.
As an action, the paladin targets one undead creature he or she can see within 30 feet of him or her. The target must make a Wisdom saving throw. On a failed save, the target must obey the paladin's commands for the next 24 hours, or until the paladin uses this Channel Divinity option again. An undead whose challenge rating is equal to or greater than the paladin's level is immune to this effect.
Therefore, I don't think it's appropriate, in a strictly RAW ruling, to apply the Turn Resistance or Turn Defiance that creatures like the Topi or Ghast have to this ability.
Control Undead is very similar to Turn Effects
Although I don't think it's appropriate to treat these effects identically RAW, I do understand why your DM grouped them together. Virtually all other Turn effects that are in this game come from Channel Divinity Options provided to Clerics and Paladins (and similar features given to NPCs and monsters). Both Turn Undead and Control Undead involve Wisdom Saving Throws applied to Undead by people using their Holy (or Unholy) power against them.
So while I don't think this is a RAW decision that your DM made, I'm inclined to respect it in practice due to the similarities both in the source and mechanics of these features, and I might make similar rulings in my own games.
No future applications of Control Undead confer Advantage/Disadvantage
Directly related to the above is: when I recast control undead on an undead that I already own, does he have to make the saving throw again, or do I have an advantage somehow because I already own him?
The feature does not specify any such feature, so you do not gain any benefit under these circumstances. The only circumstance under which you would confer Disadvantage on their Saving Throw is if a different feature or spell is causing it.