Yeah, it can be pretty anoying for some of us with the OCD
I do the following trick:
1. pause the game
2. start building fortification(or any other building) until you fill all the empty spaces in desired hex
3. press pause on all those fortifications so they don't start to use any ind goods or money
4. select the space you want to use for port (or what ever, I use this for anything as I like to arrange my buildings inside hexes the way it pleases my eye
) and click scrap on that fortification
5. unpause the game and wait until the desired location becomes empty
6. pause the game again
7. build port in the desired (now emptied) location
8. scrap all the remaining fortifications
9. unpause the game
...this made me think it would be good to ask BG to make the building location selection possible in SR1936
EDIT: damn, Balthagor posted while I was writing this
if it is possible to change the construction hex or direction, it will be good to know. 
