Electric to be said:
If I'm not mistaken, don't all forces act like they move through the center of mass in terms of translational motion (ignoring rotation)?
If you're viewing the object as a single object, yes, you can treat translational forces as if they were exerted directly at the center of mass. But that doesn't mean the are actually, physically applied there; it just means you can treat them that way at that level of analysis.
If you're viewing the object as a collection of interacting particles, then the "fictitious force" in the non-inertial frame is applied to each particle equally; actual applied forces are applied at, well, the particle to which they are applied.

But then you have to model the interaction forces between the particles as well in order to see how the object as a whole moves. That doesn't seem like the model you have in mind.
Electric to be said:
I understand that there still would be a torque about the center of mass, but this would be because one of the forces (the real one not going through the center of mass) points in a direction off center and has a lever arm
Yes.
Electric to be said:
and not because 'some' of the applied force goes into rotation and some into translation, correct?
No. Some of the applied force has to go into translation; otherwise the center of mass of the object would not move. So the full applied force is split, for purposes of analysis, into two pieces, a translational force and a torque. The former moves the center of mass; the latter induces a rotation about the center of mass.
Electric to be said:
in this case, the fictitious force would have to be the same magnitude, and opposite direction.
Same magnitude as the translational force; not same magnitude as the total force (including torque). If it were the same magnitude as the total force, the center of mass would not be at rest in the non-inertial frame.
Electric to be said:
The net torque would just come from the fact that the fictitious force acts at the center of mass (like gravity) and the real force has a lever arm.
If this were the case, the center of mass would move (see above).
Electric to be said:
using this new 'inertial frame' would have the exact same
calculation for change in angular momentum as if the axis was fixed at the center of mass and the same force was acting with the same lever arm, so basically the need for these fictious forces is removed.
No. See above.
Electric to be said:
However if it was about some other axis not through the center of mass, then fictitious forces would become part of the calculation (since then they would have a lever arm) .
I don't understand what you mean by this. You don't get to pick the axis about which a torque is applied: the direction of the force plus the vector from the center of mass to the point of application together define a plane, and the axis must be perpendicular to that plane and passing through the center of mass.
It looks to me like using a non-inertial frame is confusing you; in that case you probably shouldn't do that. The analysis can be done in either the inertial frame in which the object is originally at rest, or the inertial frame in which the object's center of mass is at rest after the force is applied. The first of those two is probably the easiest to grasp intuitively: you just apply the off-center force and see what happens to the object.