1 - technical features of both engines: while the Willys L134 "Go Devil" with its 2.2L displacement, a higher compression ratio and a more rev-happy (well, sort of) nature could seem quite obvious, instead of trying to upgrade the Model T's 2.9L engine with a slow-revving nature and a somewhat pathetic (for our modern standards) compression ratio, it's also worth to notice there are some resemblances. It's also worth noticing there are similarities, such as both following a very similar water-cooled 4-cyl sidevalve layout and featuring a 3-bearing crankshaft, which could render a Willys MB suitable to feature a Ford Model T engine with high-compression head and pistons, a stroker crankshaft, a camshaft with an optimized profile, a better carburettor, among other improvements which were already tried and proven by early hot-rodders way before the V8 craze took over;
2 - familiarity of the military personell: even though the Jeep featured a cockpit layout more similar to a modern car, many of the military personell of the United States and other Allies during WWII had their first experiences with motor vehicles on a Ford Model T and its very own arrangement of pedals and levers. While the Jeep revolutioned the market rendering 4-wheel drive a more common feature on utility vehicles, it's worth to notice the Ford Model T retained its foothold as a workhorse among some people who eventually refused learning to drive something else well after WWII, given its influence on a worldwide basis. Sure there were those soldiers unfamiliar with driving at all, who could easily stall while trying to drive a Jeep for the first time because of the clutch pedal, so the setup of the Ford Model T with its automatic clutch could've been a blessing to say the least;
3 - suiability to harsher environmental conditions: the Jeep featured a more conventional ignition, so it was a quite critical aspect while fording (no pun intended) a creek for instance, as a distributor is way more sensible than the commutator of a Ford Model T. Both a distributor and a commutator follow the firing order, but the distributor gets high voltage from a single ignition coil fed by the battery, and then feeds each spark plug cable according to the firing order, while the commutator feeds low voltage from the magneto to individual coils also according to the firing order, and then each coil feeds high voltage to the spark plug cables;
4 - technical suitability of 4-wheel drive regardless of engine: featuring a different engine wouldn't render 4-wheel drive unsuitable to the Willys MB Jeep, just like many modern retrofits have proven, yet an almost forgotten experience of 4-wheel drive conversions to the Ford Model T such as those done by Jesse Livingood have already proven a seemingly ancient engine design was not a problem at all. While the all-around drum brakes of the Jeep were better suited, in contrast to the Model T which resorted to a bands setup at the transmission for the main braking and drums at the rear wheels for stationary brake only, it's worth to remind the Rocky Mountain brakes which resorted to the stock drums to supplement the weak transmission brake on the Model T;
5 - the Jeep had been also made by Ford during the war effort: considering other military vehicles which had different engines according to the manufacturers who provided them during the war effort a reasonable circumstance, and Ford having also made the Willys MB Jeep yet renaming it Ford GPW, it would make sense to use one of its own off-the-shelf engines.