Currently, I’m using Unity 2018.2.0f2 and I can guaranty that Unity, at least in that version, isn’t able to manage its lightmap system properly.
When I look at the OV Overlap, I’m seeing what’s supposedly overlapping… and that’s bogus at best.
First, the biggest issues comes from how Unity manage the Lightmaps UVs islands alignments within the Lighting engine system.
It does it on a per-mesh basic regardless of whatever Generate Lightmap UVs is active or not.
If ALL the assets on the same lightmap are similar in size, the issue won’t be seen much, but if the assets have quite the variation in sizes, then the UVs generated for the Lightmap will be screwed beyond saving regardless of the Lightmap Parameters set on the renderers in the scene.
First, let’s show an example of who bad the system manage the UVs, currently:
Let’s start with an example. I made this semi-modern medieval building by modeling (including a clean manually optimized UVs unwrapping) pieces that were assembled in Unity. The main reason why I did it as a modular assembly is because I can create multiple buildings with the exact same pieces.
Now, with a Lightmap Resolution of 16 Texels per Unit (which is at least 2x more than I would normally allow to such a simple asset that isn’t looked up as close )… Let’s see the overlapping.
If I the lightmap to use my own UVs (disabling the Generate Lightmap UVs option) :

Ok. It returns us a warning that 110 object have overlapping UV’s. We can see that some parts are overlapping in the Scene view. What if I use Generate Lightmap UVs then?

Sacre-bleu! Isn’t that worse?!? Now the warning tells me there are 143 objects with overlapping UVs.
Now, let’s see what the Lightmap UVs actually look like…
The best case was with the option Generate Lightmap UVs disabled so let’s start with it.
Mmm. The light map basically used quite a small bit of the available space. Not only that, but you can see that some stuff is really tiny in the space.
By the way, this test was done with Lightmap parameters set so that the big parts (walls and roof) are at “Medium Resolution” while the small parts (doors, frames, windows, etc.) are set at High Resolution. Fact is that I try with both at Medium and with the one I just mentioned and the size of the UVs on the Lightmap were identical in sizes.
Let’s take a closer look at the part, in the preview, that sounded like it was really overlapping in both cases : The windows.
Okay, the UVs are like what I manually applied in the 3D software, but mirrored in both X and Y.
(I added a screen shot of the UVs in the 3D software, the mirrored it in both X and Y to display the similarity.)
The parts that aren’t visible in Unity’s Overlay Lightmap UVs but are visible in the 3D software are parts of another window model that isn’t used in the scene right now.
But, we can see the problem there. The UVs island on the Lightmap are too close. If I was in controls of those specific features, the 2 solutions would be to regenerate the UVs in a way that doesn’t stick them as close as that or to allow the UVs island to take more space in the Lightmap so that there’s at least enough space (padding) between each island, right?
I tried many things by changing the Lightmap Parameters and allowing an higher resolution. Didn’t change anything unless I put a resolution that is far too high. Raising the Lightmap Size didn’t changed neither.
On thing I do find quite strange is how the lightmap resolution in the Scene Lightmapping Settings has some extreme change in the way it handle the lightmap uvs. The change between 2 and 8 were noticable for all the sizes. Between 8 and 32, the changes mostly only affected the big assets like the walls and roofs while the small assets seemed to keep it really small in comparison. (There’s maybe a 20% difference in size between 8 and 32 for the small asset while the big asset tripled in size.)
When made it pass 34, suddently, the UVs island of the lightmap extend onto the whole area (filling that big black square spot you can see in the screenshot above.
So, adding more available space in the UVs is, at most, impossible to predict unless I start raising the resolution through the roof just so that the original padding from the UVs can enough to avoid Unity to think something is overlapping.
I’ll post this now and will follow with another post as I can’t post more than 5 image per post.