As you've identified it is possible to have perks, virtues, techs and buildings provide an empire wide boost to an improvement. If you want to have a building boost an improvement only for one city then it isn't directly possible. You can have buildings boost Resources though.
If you want to make a building boost farms only for a single city, I've implemented a crazy way to sort of fake it. It involves spawning hidden resources under every farm and having the building boost that resource.
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But I should address your original design question rather than derailing it with technical information.
With respect to if Improvement buffs should be on the tech tree it depends on what you're trying to do with your design. I know that is a useless answer but design requires a holistic eye and without more information I honestly couldn't say what you should do.
My current approach moved away from having Improvement buffs on the tech web because I wanted try and make Science less powerful relative to other yields. A tech that unlocks a building will require Science and Production to generate benefit, while a tech that boost an improvement just requires Science to generate benefit.
That may not be the right approach for you. It closes off some useful design space that you may want to tap into.