I play with the swap : University costs 7 doubloons and Factory costs 8 doubloons.
But when playing whit expansion 1, do you swap some buildings from the expansion ?
No, I leave them unswapped, even in the base game. Swapping these two and making the Factory same cost with the Harbor gives no incentive to buy the Factory at all. At least, at $7 you do have an incentive to buy it. The University is useless anyway, even at $7; it should drop to $6 or $5 to have some value for money.