Sure thing - we’d be happy to provide you access. It’s a commercial project though, and I don’t want to make too much work or friction for you.
In the meantime, I also built 5.6.1 from source, and applied the latest updates as a patch from your GitHub. The results were the same, but I believe that I have isolated the cause of the phantom shadows to painted Foliage, which uses HISM.
I deleted them from the level, and the compression artefacts and also the phantom shadows disappeared, leaving a great bake in their place.
I can try to replicate the issue, but it looks like the foliage actor may be the cause. We’re using VTs for, and some parallax occlusion as the only two unusual features on our Foliage meshes.
Perhaps I can also try to replicate this issue in a simplified project, and send that over.
I will also try to catch some of the crashes, and report back
Update:
I also tested the crash in the other level, and found two causes. The simple one was a duplicate instanced foliage actor, that wasn’t associated to the level but did contain geometry. It might have been because the instanced foliage was split between streaming levels. The error was here:
The more complicated one seems to do with Landscape RayTracing data.
The crash ends at check(RayTracingGeometry != nullptr) in RayTracingMeshDrawCommands, but steps up to LightmapRenderer.cpp, line 1347, with RayTracingMeshProcessor.AddMeshBatch(MeshBatches[SegmentIndex], 1, nullptr);
I believe it is to do with setting up the landscape for baking, but I haven’t found what’s missing yet. Any tips for digging deeper?
Update 2:
I’ve had some luck fixing the phantom shadows with r.RayTracing.InstanceBuffer.RLE 0.
'I’ve also had some luck fixing the landscape crash with r.RayTracing.ResidentGeometryMemoryPoolSizeInMB 800.
I’ve found a crash or two to occur at different steps, which I’ll look into. But in short, I think the phantom shadows were from the foliage transform upload bug. I think the random crashes seemed to be a raytracing geometry memory pool issue, but I’ll keep looking to see if there were other issues.
Either way, I’m able to get bakes, and the project is moving along 
Update 3:
Handling the foliage actor’s InstanceLightShadowUVBias is currently causing a crash on another level. I couldn’t find it being calculated or set above on a quick glance, which might possibly mean that InstancePayloadData.Emplace(InstanceGroup.InstanceLightShadowUVBias[InstanceIdx]); will always crash. I guess I’m missing something, but I’m looking into a fix.
Update 4:
After a day of internal screaming and testing, I have extracted these facts that may help developing the tool, and also may help other GPU Lightmass users:
Landscape Foliage may cause dense shadows, as yujiang.wang already mentioned. using r.RayTracing.InstanceBuffer.RLE 0 will help.
Landscape Foliage will also cause a crash if any of the foliage types are set to use Volumetric Lightmaps, because the code tries to write an InstanceLightShadowUVBias that isn’t there (I believe). This crash might just say something like Array Index out of Bounds as the crash message.
First Bounce Ray Guiding and possibly Irradiance Caching causes errors, but not consistently. These errors don’t show up during the preview, but appear after the encoding as black landscapes and heavily artefacted lightmaps. The best that I can figure for now is that it happens in levels with more complex lighting setups, as I don’t see this in new or small levels. I have found that disabling them results in cromulent bakes. I do miss their ability to throw light into internal scenes, but getting shippable bakes is, for me, the priority, and I’ve achieved that.
I ran out of ray tracing geometry memory a couple of times, and I found that r.RayTracing.ResidentGeometryMemoryPoolSizeInMB 800 helps that. You may need a larger value, if your scene is colossal.
GPULM looks great, and we would love to keep using it. If it is helpful, we’ll keep testing 
Thank you again for working on it! It is a saviour for games that need to target 90-120fps on a range of performance targets, but want to look like they’re from this decade! For us, the final missing piece is the ability to bake HLODs, but that is not a trivial thing to solve, I believe.