Slitherine

In the manual,"Regions of allied nations trade use the same rules as apply for internal trade (or trade with a client state), making it more likely that trade goods will be exchanged."

However, the cost of imported goods of allied nations or a client state is full cost instead of half in internal trade.

Besides, my trade acumen is 10 while their acumen are 3 or 5. My regions still import goods from their regions instead of my regions which are also in trade range.
I'm confused.

Few bits to this.

If you are allied then their regions are treated as your own territory for trade purposes - otherwise there is a malus against trading outside your own boundaries.

But, you still pay full cost (as opposed to the 50% for a purely internal trade) - of course so do they. This is why the AI is often very unwilling to make an alliance with a faction that has very high trade acumen.

which brings us to ...

in the situation you describe, yes the balance is to an in-faction trade (in part due to the acumen) but there is a random element (which is why trade income can vary a lot from turn to turn)

I usually have like between 40%-60 negative in diplomacy because "we don't want to be flooded with your cheap goods" . Having a lot of ressources that other nations and tribes don't have should a positive thing for them to deal with you not the other way. It is just so annoying nation like Carthage who usually had really good relianship with deserting and Iberia tribes can't establish cooperation and alliance with them.

Only cooperation have this modifier. Alliances and Client-states should not have that.