There's not a whole lot of surviving documentation on WWI aircraft, but supposing the Fokker Dr.1 represents engine horsepower (at 110HP as one source cites) of WWI aviation engines in general, I'd guess the biggest issue would be cooling. Advances in engine design, engineering processes, and material technology allowed rated power on engines to soar by the time we reached WWII. While it's possible to dump more fuel and air at once into larger and more numerous cylinders, thermodynamics aren't on vacation and you need to dump the waste heat overboard if you don't want your pistons to take a forever break. The Wright 1820 which saw use on B17s developed something like 700 rated HP depending on your model. I'm not sure waste heat scales linearly to HP but it seems intuitive to say it should, and at any rate that's a lot more waste heat than you saw in WWI planes in which could probably get by on a single cooling intake for both engines without a huge increase in front profile. So the issue for me seems to be that you just need more space in your frontal profile for cooling, which is made easy by having a full pod for each engine. There are some ways to mitigate cylinder heat, like running rich of peak and having oil coolers, but you can only mess with your F/A ratio so much before your engine can't burn fuel anymore, and oil coolers still take up some of your front profile so you're still canceling out some of your lift to cool the oil.
Some other things could have had an impact as well; assuming your design doesn't have the crank running through the rear of the engine so that both propellers are powered by the same engine (which means you've lost the HP of an extra engine), you need more engines, and more cylinders means the engines need more cooling air. You could run ducting for ram air into the nacelle , but that means a bigger nacelle, which probably already got bigger when you stuffed the second engine into it. Push engines in push pull configurations already lose some efficiency from operating in the disturbed airstream from the puller props, and the efficiency you gained by losing an engine pod is rapidly being reclaimed by the inescapable tendency of this world to hate fun. I'm not sure where the lines cross and whether you've gained or lost efficiency, but I'd guess the complexity you add to the system makes it easier, if not more efficient to just make the thing with four nacelles after the previous downsides have already been added up.
A few other possibilities; a lot of WWII bombers were conventional geared and their props already came fairly close to the ground; with the pusher props located behind the pullers, there could have been some risk for prop strikes, which would probably be the easiest engineering hurdle to fix. The mounting points would have had to have been reinforced to probably slightly less than twice their original strength to hold the new engine and all of its accessories, which may have been too much put at one location on a spar with WWII engineering (decent chance that this is bullshit!).
Of course the easiest answer is that push pulls were unconventional and they may not have wanted to push something untested into production when the convention was already well tested.