Most importantly, if managed to place a marker on either one of them, which is both extremely easy and very in-character, then it would honestly be game-over. It'll allow him to freely tag them whenever he wants, and they really can't do much about it.
Actually Boruto can counter this, the Karma Seal allows people to absorb Sealing Jutsu, so Boruto (given that he already has knowledge on Minato and Naruto already) can very easily counter that.
- Sealing Jutsu: Another big thing in Minato's arsenal. He can potentially seal away Naruto's usage of Kurama's chakra with this, or just outright seal these guys away if he gets a chance.
Same point as above, Boruto can absorb Sealing Jutsu. It's dumb but hey.
- IQ: I'll let people more familiar with Bort speak on this in more detail, but Boruto is very smart. He's both book smart AND battle smart. He's very good at utilizing his limited number of clones to create leverage, openings on his opponents, or to avoid damage. He also has a lot of options to work with, such as 3 Nature Transformations, karma, among other things.
See, the Karma not only gives Boruto a power-up physically, but also drastically increases their combat skills by stacking that of the Otsutsuki. Code pointed this out as a major factor as to why the Karma is such a good powerup.
Plus, he's generally smart, and can as you said, use 3 Nature Transformations, and often combines them, e.g. Water Release to flood the area and then Lightning Release to shock everyone nearby, aka making the Jutsu stronger.
- Decent AP amps with stuff like the compressed Rasengan and his other enhanced Rasengan variants.
It's kinda stupid how much stacking Boruto can do to increase his AP, firstly the Karma which greatly increases his strength, he can naturally also use his Wind Release Rasengan which is stronger than the regular Rasengan he uses, but he can also use the Compressed Rasengan which is even stronger. But it's not just that, he can also add on the Boruto Stream which 4 clones to further increase speed and AP.
I do feel the need to mention the fact that Minato
can use the Reaper Death Seal, but that's more-so an incon and wouldn't be very in-character.
I do feel like Naruto loses either way and just sits there to wear down both Minato and Boruto.
Given that Naruto would be basically just a wear-the-other-2-down-and-then-lose machine, I feel that Boruto would gain an advantage because he can easily replenish his Chakra and Stamina due to the Karma's absorption. Meanwhile Minato would start to stagnate after a while.
