Thanks for editing the OP. The colors made it very hard to read, and I wasn't about to spend an hour trying to find a typo.
But, I think that is what you will have to do, assuming you are placing the file in the correct location (you didn't say which folder you had the file in). You are using the 'Mods' folders, correct, and not simply editing the original files in their original locations?
The Mod structure is such that if you put the file in one particular folder (in the Mods folder structure) it will replace the original game file, and if you put it in another folder it will add the content to the original.
I only have the original GalCiv2, but the Mods folder structure should be similar in all versions.
To entirely replace the game's (i.e. TechTree.xml) file, you would put the file in the GalCiv2\Mods\*(insert mod name here)\Data folder.
(Each version has its own Mods folder in its own game directory. So placing your file in the GalCiv2 folders will not affect a Twilight game - it would have to go into the Twilight folder.)
To amend (add to) the currently used (i.e.) TechTree.xml file you would would place the file in the GalCiv2\Mods\Default\Data\Techs folder.
As such, if you copy the original file, make changes, and then put in it the 'Techs' sub-folder - you will have duplicates all over the place. Same goes for the 'PlanetImprovements' sub-folder. A modified full file should always go in 'Data', while simple additions without the original content go the the respective sub-folders under 'Data'.