Agreed, it makes sense as the most powerful economically/militarily that you have to show a certain altruistic magnanimity to overcome natural distrust.

How much does changing the strategy to 'befriend or ally' help with this malus?

By itself i don't think it does anything its just there for ...

All working as intended. Obviously if you have a large neighbour with a similar political outlook or core philosophical values, you'll instinctively grow to hate them and want to fight their vastly more powerful empire. That's REALISM!

Imagine if there was a real world power that was ...

As @ Emperor0Akim put it the full Diplomatic Research gives you a +15 and iv seen gift go up to +30 via tech trading add to that trade agreement(+20), map sharing(+5 to +15), non-aggression(+10), migration(+5) you can easily get over the malus and if you have a good reputation(+7) and actually ...