I'll give an example, one similar to what I often encounter:
A tile has a bonus, +2 to research and +1 to neighboring manufacturing. This tile is adjacent to 3 connected normal tiles.
x R 0
Where x is no tile to build on, 0 is a regular tile with no bonus, and R is the research bonus tile. The 0's each have +1 to manufacturing because of the R tile.
So my options are:
- Build a research lab on R, build factories on 0. This seems to takes "full advantage" of the tile bonuses, but limits building adjacency bonuses to 2 or 3:
x 2 3
- Build a research lab on every tile, giving the following bonuses:
x 5 3
- Build a factory on every tile, giving these bonuses:
x 3 4
Or, I could completely ignore the tile and build whatever. There's no rule saying you must take advantage of these tiles, and if the tiles just don't fit into your plan for the planet, sometimes that is the wise decision.
As you can see above, sometimes the best decision is to pick one or the other, using building adjacency to boost bonuses higher. On the other hand, if I have, say, 2 tiles adjacent, one of those tiles having +2 influence, +1 approval, I will sometimes build an influence building and an approval building.
But every choice is different, every planet is different, and there's no "right" way to choose every time. How I choose depends on what I have in mind for the world, based on its location, inherent bonuses, colonization events, and what my empire needs.