He could BFR both, for starters; he's far faster than either Hulk or DOS Doomsday.
Beyond that, DOS Supes was able to put DD down with sheer brute force (albeit at the cost of his own life); current Supes is far stronger and faster now than he was then. He could physically wreck Doomsday in a short period of time with ease, and he wouldn't have to worry about Doomsday adapting on the fly like his HP counterpart was able to do. Hulk presents more of a problem given his strength, but Supes has too many ways to beat Hulk provided he doesn't play around with him. He's faster, and has more abilities at his disposal to win. Assuming Clark doesn't fight like a retard, there's no reason he shouldn't take all 10 wins out of 10 here. There's nothing DD or Hulk could do to stop him.
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DOS DD was as fast or faster (if you believe Booster Gold) than DOS Superman. Current Supes hasn't improved that much in that department. And while I do agree that current Supes, physically, would make short work of this version of DD due to being overwhelmingly stronger - it isn't one-on-one. While Supes is busy dodging or tanking DD's shots, he's got to worry about not being hit by Mindless Hulk - who is in all probability stronger than Kal.
And off the top of my head, he's recently been semi-embarrassed by two bricks in the form of Konvikt and Hercules. There's probably more, but meh. Having to deal with two of them - one which possesses incredible speed - and I can't really give Supes a majority of wins here.
Though, you explained yourself nicely and I like your reasons for thinking otherwise.