Maybe it was just me but I had some serious issues with the new reference data included in ForgeTools3.
1) It only includes the GameInfo and Mesh folders and is missing everything else. That's not the end of the world as you can find them in your install directory as well. I'm guessing this was done because the rest of the missing files don't come in a binary/non-binary variation and it cuts a lot of space down when they don't include textures.
2) RESEARCHSUBJECT_ARTIFACT_STRONGCULTURE.entity is missing from the new reference data. This is still referenced in GalaxyScenarioDef.galaxyScenarioDef so I'm assuming it was a mistake of omission. Replacing it with a copy from ForgeTools1.1 seems to work.
3) The new reference data in ForgeTools3 does not seem to work, for vanilla SoaSE at least. I was getting minidumps like crazy while trying get a working updated version of my mod. Eventually I decided to troubleshoot the reference data itself. I created two new mod folders, one including only the new reference data files and the other the GameInfo and Mesh folders from the Sins install. The reference data mod minidump when it was enabled while the Sins install copies loaded without a problem. A comparison of the GameInfo folders shows only 886 files (after replacing the missing entity in the previous point) in the reference data version while there are 896 files in the Sins install version. Dev Mode does not report any errors concerning what is missing or wrong, it simply minidumps.
I was able to get a working version of my mod working by using the install binary versions of the GameInfo and Mesh folders and then adding the modified TXT versions I needed from the new reference data. In my case though, only GalaxyScenarioDef.galaxyScenarioDef is overwritten from the stock data and the rest is new entities.
I have not done anything with the Entrenchment reference data yet. The above refers to the vanilla Sins data solely as I have not confirmed any issues with the Entrenchment version at this time.
Hope this helps anyone having issues updating mods with the new tools and helps the Devs track down any problems.