As far as I understand it - and please, someone correct me if I have this the wrong way around - the funding percentage applies to an increase in capacity by city. Each city's research capability is determined by a combination of specialists, trade, and buildings, with added modification based on civics. By throttling funding up to 100%, it means that each city is doing everything it can to add to the research effort - that is, it's working at 100% of its capacity. But if your civilization is bringing in more cash than the cities can consume based on their specialists and buildings for research, the extra is funneled back into your treasury. Perhaps modification of building or specialist effects would do the job, but that could radically unbalance the game.