Think of New_Civilian's MyMod modpack: there you have to complete gauss tech tree before allowed to research sonics. Now look at FMP: there are multiple branches, from laser to fusion, from mutant to MIB. You could force to complete one branch before allowing the next to be researched.
Yeah, you could, but if I'm a player and I decide halfway that I want to focus research on something else and discover that my research path is locked for no apparent reason (you'd need to explain somewhere to the player how it works for him/her to understand the consequences of the choices), then I'm going to be frustrated.
Or you could say, "ok, player got that MIB stormtrooper armor now, so doesn't need synthsuit too. Make good use of what you have."
But that's why there's money and alloys/Elerium in game: you can only build what you can afford using the limited resources available. Make good use of what you have, but if there's only 1 item to build since the similar ones are locked out, then you're forcing the player into a single choice.
For instance, if I choose sonic over gauss, and then later I fail to recover Elerium/alloys from UFOs to build those sonic weapons, then the game design has just placed me in a very difficult tactical position, if not impossible because plan B (gauss) is locked out and all of these Mutons are trashing my soldiers armed only with conventional weapons.
I can imagine using this for straight up upgrades to tech. Make laser rifles MKII that are a bit better than normal ones but take the same resources. No point of keeping old versions in manufacturing list because it's just clutter at this point.
This is a good way to add upgrades to weapons. Research aiming sights and all of the lasers are replaced with improved versions.
Modder should have control over the mod and it's mechanics. It's a game design issue. You may want to pace the game right, make it challenging in a some way or use it in narrative. Buying odsolete equipment for what is a borderline exploit... not so legit.
If you say that the modder needs to have control, then he's also entitled to decide if the borderline exploit should be present or not. And if there's so much of an issue with the exploit, then there are easier ways to fix them by editing the equipment's stats.
