I think this is where you are going wrong. ALL of the force acts to translate the centre of mass.
F=X, if X+Y=F then Y=0
Picture 100 particles. Any configuration. Some glued together rigidly. Some totally detached. Some attached by elastics.
Now apply a force upwards on any particle or particle group. Call that force F.
F will equal ma, where a will be the acceleration upwards and m will be the mass of the system.(elastics and all)
Redo the math for the same thing adding a mass the size of Jupiter to the system where Jupiter is 100 miles away and is totally unaffected.
F will equal ma, where a will be the acceleration upwards and m will be the mass of the system including Jupiter.
Redo the math for the same thing adding a mass the size of Jupiter to the system where Jupiter is 100 miles away and is the only body affected by the force (upwards again whatever that means in the reference frame you are using)
F will equal ma, where a will be the acceleration upwards and m will be the mass of the system including Jupiter.
If F accelerates the mass in translation and in rotation it doesn't matter.
F will equal ma.
(if you sum the "rotational accelerations in the upward, or any direction they will cancel out)
If this seems odd it is probably because you intuitively feel that since F may be doing work to stretch elastics or cause rotations etc that maybe some of F is "used up" in this regard.
It is not.
What is different and does need to be divided up is the energy or work done by the force F.
The work done by F is very different in each of the above cases.