Ah. Wonderful. I was afraid that might be the case, but I wasn't sure since I didn't find anything about problems with compatibility. Maybe everyone else here is just familiar enough with the tech trees already that it didn't warrant mentioning in the year and a half or so since 2.20 was released.

It's not really the answer I was hoping for, but still, thank you. At least now I know why.

I may have found a fix/workaround to get Galactopedia working.  Galactopedia appears to crash with UE2.20 because ...\Twilight\Data\English\StarbaseModules.xml includes the StarbaseAbility 'RepairAssist' (on line:28).  The basic idea is setup Galactopedia to read its info from a copy of the asset files that have the one offending line changed:

    1) Edit ...\Twilight\Data\English\StarbaseModules.xml, TEMPORARILY change 'RepairAssist' to 'RepairSB' on line 28.
        This should allow Galactopedia to launch so you can modify where it looks for files.
    2) Copy the required game asset folders into the Galactopedia folder:
        Folders: Data, Gfx, DarkAvatar/Data, DarkAvatar/Gfx, Twilight/Data, Twilight/Gfx
        This appears to work, not sure if other folders are needed/useful
    3) In Galactopedia  under 'Source' -> 'Game Folder...':
        set the "User-Selected GalCiv2 Installation Folder" to the path of the Galactopedia folder
    4) Revert the temporary change made to StarbaseModules.xml
    5) Restart Galactopedia

Now the game files should be unchanged, but Galactopedia should be reading from a copy of the game files with this one modification.  I made one more minor change to the Twilight\Data\English\StarbaseModules.xml that is now in the Galactopedia folder: On line:26 I modified the Description to remind me that the description in Galactopedia differs from the actual game files (I appended "NOTE: Does not repair starbase").

For first time Galactopedia use: I seem to remember that the first time you launch Galactopedia it may ask for the path to the install files, if that is the case then there should be no need for the temporary edit and reversion, just copy the folders into Galactopedia, edit the correct StarbaseModules.xml file in Galactopedia, and then tell Galactopedia to use it's own folder as the install path.

I hope this workaround actually works for you.  I find Galactopedia indispensable when I play (I keep it open on one monitor when I play and refer to it often) and hope that someday the source code is updated to work with the community update or even be included directly in the install.

I don't think Galactopedia works directly with mods, my understanding is that you can have numerous mods in your mods folder and only when you start a game do you decide which mod to use.  From what I can tell Galactopedia works independently of your game and has no way to know which mod you've selected.  It reads the data files directly (you can use it when GalCivII is not running), and I don't know of any way to tell it to read from the mods folder (although I could be overlooking something). 

The only way I know of to get Galactopedia to use a mod is to overwrite the files copied to the Galactopedia folder with the modded ones, folder by folder.  I agree this would be a hassle if you are regularly modding data files (I've only modded the UI). 

One possible solution would be to use a program that keeps folders in sync 1-way: when you modify a file or files in your mods/modname folder it could be set to (manually or automatically) copy file(s) to the Galactopedia/Twilight/... folder to keep Galactopedia in sync.  I've used open source freefilesync for this purpose on other projects - save a 1-way sync as a batch file and then just 2xclick its shortcut to run it and sync.  A bit of effort to get the workflow in place, but could be useful.