It violates your requirement but you could have great works that are located somewhere specifically, but that have empire wide effects. A solar system sized particle accelerator would advance science everywhere but you only really need one. A single Dyson sphere could change an empire's energy usage. The location doesn't matter other than putting it somewhere unlikely to be invaded. It could even just always occur in your capital location

For science, improving your intergalactic internet bandwidth could be a non-localized development project.

Another abstraction could be the investment is on talent identification and recruitment. If a fully developed world produces a super-genius every 100 years, then in a 100 planet empire one of them is born somewhere every year. But if that's in a mining camp on a outer world, does your empire find him? The quality of your pilots would be a function of how many people are evaluated as small children to be put into the special pilot training schools. Actually building pilot training schools is a rounding error compared to the process of filling it and can be ignored.

If you don't want it to be planet-specific, then maybe Buildings are the wrong type of thing (though the parallel to Civ buildings is a good reference point), as any building would HAVE to be built on a planet, even if it had empire-wide effects. Instead, maybe there could be agendas (edicts, policies, platforms, decrees, idk what is a suitable word) that could be focused on. Like the general implicit goal of the empire, spread through propaganda and stuff.

So the Player (emperor) is like hm I need to beef up my science so I'm going to deploy the propaganda that promoted education, research funding and interstellar exploration.

This could have the same effects as any building (+5 sciences a turn; +2 to science; -4 to killing aliens) and not require clicking on planets. The only difference would be that it's not a permanent bonus, like buildings (pretty much) are. Maybe individual planets could have (invisible) meters that fill as you stay on the same propaganda train, and when they fill up that planet gets a building or something that provides a bonus to that specific ideology.

...Though, that's back to planet specific buildings lol

You could charter organizations, that's nebulous but creates something concrete. The Free Starshipwright's Guild are a secret society that helps share shipbuilding knowledge between planets. The Order of Leibowitz preserves knowledge and industry on planets during conquests/nuclear bombardments/etc. the Big Brother Program recruits impoverished youth into propaganda work.

One option is they need a big capital or imperial support infusion to get off the ground. Another is that you can charter a certain number of organizations at a time, but it takes a while for critical mass to be achieved. There could be levels of success where an organization needs another big investment to go from a special interest group to a galactic presence.

Or this could be a reward for having a good council, occasionally the best advisers will ask your permission to leave and start an organization, and you have to decide whether to keep them on or create the organization.

What about this: Organizations have "levels" or some more flavorful name. You invest points to level up organizations. These could be things like "provide an office on every world", "assign a galactic noble as director", "Provide tax exemptions to members". Possibly organizations decline over time without intervention, so as you get bigger you need to spend more maintaining the existing charters. Possibly random events harm the organizations via scandals.

Once an organization is at the top level, you'd need to charter new organizations to get more benefit, and maybe the additional organizations are more expensive. "Human Advancement Project" provides a science boost and is popular (and so cheap). "Cult of Brains in Vats" also provides a science boost, but people need more prodding to join. That way cost scales the higher the bonus is.

As for multiple planets, I'd just make population a denominator in calculating the bonus. A level 2 organization provides full bonuses to an individual planet, but you need level 20 to get full bonus to a 100 planet empire.

If you go with organizations and a decent resource pool you could simply have the player allocate % of resources to each organization with the option of building a new one. Have a spread button to evenly spread resources over all organizations would make it very simple. Then you would would let the resources build over time till they get high enough to build the next level of the organization.

This gives simplicity and flexibility. A player could spend time setting the percents to force a specific one to build much faster than the others or spread them so that over time the bonuses from each organization would go up.