I haven't seen any real mechanically difference between normal techs and specializations. Aside from the multiple choice part, the only difference that I've seen is in the way they have been used thus far. The specializations might offer things like smaller weapons, cheaper weapons, or better weapons (offered in percent improvements). For instance, a specialization might reduce the size of all missile weapons by 20%. Normal techs tend to offer new things instead of improvements to existing things. For instance, they might unlock stingers or harpoon missiles.
I suspect that if you wanted to mod things, you could make the specializations unlock different ship parts and planet improvements, and make the normal techs give bonuses only. I'm not a modder, but I think you could make a line of techs that combine all weapon techs into one branch. With that branch, you might be researching weapon techs in general, and for each specialization, you choose if you want lasers, railguns, or missiles. Each of the normal techs might simply be percent increases to firepower or something.