Instead of 2 stations side my side or 1 in front of another station you can split them up by more tiles. Since industries rarely (or never) are adjacent to each other it should be possible to build a station on each side of the industry linking them with the CTRL placement you did with Parnpool west. Like the setup in the picture you attached, but all grouped as one station. One or two tracks on the left and one or two tracks on the right, scenario's where this cannot be done are extremely rare. There is always the bulldoze tool for cities too :)
I'm not sure what the max size of a station is by default but i never changed it and rarely get that message and i usually build huge hub stations on cramped spaces.
You really should not have any problem putting stations side by side with space, towns or industries in between them. If you do i'd like to see a screenshot of that scenario and i can probably help you out with the placement.