Still not sure what you are doing.
I have just tried the following.
Created a custom tree based on the Drengin, called it Elves. (Select Mods, create new tree)
Selected Iridium tree, copied Marketing Tech, selected Elves tree, pasted onto Intimidation (first tech in influence) Saved tree.
Selected Snathi tree, copied Recovery Tech, Selected Elves, Pasted onto Engineering (first tech in engineering) Saved tree.
Fired up GCIII, selected Elves tree as my custom tree. Both new techs are available to research.
Both when researched give the appropriate access to building etc.
Another problem, when options are a prerequisite, it doesn't copy properly. You have to manually enter all 3 options.
Can you elaborate?
At present you can't copy or paste Specialization techs.
Hope this helps.