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You are overthinking things.
You would not notice any difference in height, I doubt that this will be finished floor level (happy to be wrong on this) so you still have underlay and flooring to go on top smoothing things out more. If you really must do something for your own piece of mind a good bead of construction adhesive (gripfill, sticks like sh*t, CT1 etc) on the top of the joists before laying the boards this will hold the floor tight (many structural flooring systems require it) and take out a lot of the discrepancy.
The chipboard sitting on joist hangers will not affect squeaking. If you don't want the floor to squeak you need a good amount of PVA applied to both the tongue and groove at each joint squeaky chipboard floors almost always mean someone has cut this particular corner.
This is probably a very common problem, but I have don't know what the common solution would be. As a guess, I reckon in the trade one would ignore it and accept the 3-4mm in the flooring. One possibly crazy option to consider, router out the underside of the chipboard as you go to clear the hangers? Or as its softwood could you depress them with a hammer?
I'm not thrilled about either idea though.