So the finished interchange will be a 4-level directional stack.
Good. A directional stack in that location is not really an extravagance considering two of the existing flyover ramps will remain.
I think it does make sense to replace the existing SB I-49 to WB I-40 ramp with a new ramp that will join with a new NB I-49 to WB I-40 flyover ramp. That will reduce any merge conflicts with I-49 traffic entering WB I-40.
The mainline I-49 overpasses are WAY up at the top of the stack.
In retro-fitting an existing Y interchange into a full stack they have don't have any other choice. What else could they do? Tunnel the main lanes of I-49 under I-40?
It's not necessarily a bad thing to place the main lanes of one highway at the top level of a 4-level directional stack interchange. Others exist that have done so. the I-45/I-30 interchange in Dallas is one example. The Bush Turnpike and US-75 in Plano is another. The US-101/CA-110 interchange in downtown LA is old but iconic.
Anyway, when the I-40/I-49 interchange is completed it will no doubt be used a lot more by motorists coming up I-49 and going into Oklahoma as opposed to leaving I-49 South of Fort Smith and taking other roads to reach I-40 in Salisaw. There are 7 traffic signals along the 4.5 mile stretch of US-71 between the future I-49/US-71 interchange and I-540. Once I-540 enters Oklahoma, turning into US-271, there is at least a couple more traffic signals along the way in towns like Spiro. Taking I-49 up to Alma to pick up I-40 might indeed involve some back-tracking to go West into Oklahoma. But that's going to be a lot faster than any alternatives.