I have successfully mode a Total conversion of Star Trek Armada 2 into the Fleet Operations engine that works in GOG Galaxy.
Here is alink to the mod posted to my Google Drive.
h t t p s : / / drive.google.com/file/d/1En3gsRaTN52KMWWuXbST0C1wCPTFFoLK/view?usp=share_link
{Due to forum restrictions remove link spaces.}

GOG Galaxy instructions.
go to your GOG Armada 2 installed directory and do the following.
5/8/2023 Revision
1:Create a Data Folder in your Star Trek Armada 2 Folder.
2: Move your Armada2.exe into your new Data folder.
3: Delete everything else.
4: Extrace the zip file into your Star Trek Armada 2 Folder.

Now you are good to go.

If you did everything correctly it should look like my example image.
The way the mod works GOG Galaxy will refrance the Armada2.exe included that will hook the Armada2.exe you placed in the Data Folder.

Meaning you need to own Star Trek Armada 2 for this to work.

Updated 5/11/2023 fixed fleet selection and included multiple update mods.
Race Specific flairs, Fusion Script, A2 Upgreade.
Multiple Fixes fleet selection and wire frame issues and unit selection and icon bugs.

Downloading now and very excited to try this out! I've been hoping someone would do this ever since the GOG release.

Also, you might want to upload this to some other places, too (like moddb). Can't really trust forums (or GoogleDrive links) to stay around long-term.