When you put tech of the same type right next to each other, and by that I mean like Photon Cannon, Hyperdrive, etc, they have the same border colour, they give each other a boost.
This is called the Adjacency Bonus, and for the most part, it is actually quite simple, even if I did find it incredibly hard to get my head around in the first place.
Ket is a very patient man luckily.
There are 2 types of bonus, Additive and Multiplicative, Additive is used for such things as Light Years on the Hyperdrive upgrades, an Additive Bonus is 6%.
Multiplicative is used for Percentages generally and is 4%.
Each bonus type has a lesser, 5% for additive and 3% for multiplicative.
The issue at the moment for working out which modules and stats are lesser and which are not is that I do not personally know where this indicator is found in the files so I cannot know exact numbers for bonuses and so cannot give you fully accurate builds as far as the DPS and so forth, but by knowing how the basic system works and working within the lesser and none lesser range, we can guide ourselves for in-game testing, which I've done a fair bit of for working out layouts.
As for how the bonuses are applied.
Each module has its bonus worked out and then they are all totalled.
This bonus is calculated based on what is directly touching it on its 4 sides, it is essentially, Adjacency Bonus multiplied by how many sides are touching plus lesser adjacency bonus multiplied by how many sides are being touched by lesser.
For example, with Hyperdrive Upgrades.
If you have one module that has a light year range of 217, that is touching a module with 246 light years which is then touching a module with 232 light years.
You start with the first one, the first 1 is touching the second one, so has 1 account of the additive adjacency bonus of 6%, so 217 multiplied by 1.06 is 230.02.
The second module has a stat of 246 and is touching both the first and third module, so this is multiplied by 1.12 for 275.52.
The third module has a stat of 232 and is touching the second module, so just one adjacency bonus for him, so 232 multiplied by 1.06 is 245.92.
Add them all up for 751.46, add the hundred on from the main unit for 851.46.
Due to some rounding at times it may be off by 1 or 2 light years, but it'll pretty much say that on the dropdown tooltip for your ship bonuses in the inventory screen.
If you want to learn more about Adjacency Bonuses, I have linked Ket's original guide on Steam which details how the system works.
It is from Atlas Rises, but Ket has confirmed that the system still works this way, with the same 4% multiplicative, 6% additive etc, just what is lesser or doesn't have a bonus etc is different and yet to be worked out.