So just to understand the mechanics better then, can one of you please explain where your getting the "half are free but half are wasted" thing.
Basically the way it works is that you pay 1 bc for every RP you produce "on-planet" but for any global bonus research you pay 1 bc for every 2 RP's of "off-planet" bonus production.
To take an example lets say you have Xeno Lab on your home planet on a 300% research bonus tile for 8 RP plus a "bonus" 24 RP. Along with this you also have 24 RP's of research from your civilization capital and you also have your tech capital for an additional 100% research bonus.
So this gives you a total of (24+8+24)*2 or 112 RP's of "on planet" research for which you will pay (assuming sliders at 100% research and 100% utilization) 112 bc's.
If that's all the bonuses you have then you will see a planet production of 112 RP's and on planet spending of 112 bc's plus whatever other maintenance you have for other buildings on the planet.
However, let's also say that you happen to have a fully populated economic SB giving a 24% SP/MP/RP bonus to the planet along with 39% from a maxed out research mining base and another 37% (randomly selected to make the math easy) of racial ability. So you will see the 24% SB bonus listed in the planet details screen. In the racial abilities listed in your civ manager you will see your base racial abilities of 37% plus the 39% from resource mining for a total research ability of 76%. So your total global research bonus as it applies to your home planet is 100%.
In this case you actually see the planet producing 224 RP's while the planet spending still only shows the 112 bc's cost of the "on planet" research. However if you go into the domestic policy screen under expenses you will see a cost of 56 bc's for Bonus Production/Research which is the cost of the extra 112 RP's of research due to global bonus.
So the bottom line is that you pay 1 bc for every RP produced "on planet" whether it's due to bonus or not but you only pay half of any RP's produced due to global bonus including econ SB bonuses.
This actually brings up a bit of a pet peeve of mine and that is that although I will use an "all factory" approach in mid to late game I absolutely think it's a mistake to totally ignore research building, particularly on bonus tiles and particularly early in the game. Yes, I agree that to have sliders select between industry and research results in great inefficiencies and waste, but that still doesn't mean that you can't get higher levels of both industry *and* research by using a balanced approach versus using only one of industry or research.
The reason for this is that when you use focus to get research out of industry or vice versa to get industry out of research you lose all benefit of any and all bonuses of the opposite type. So I might have a NLC on a precusor mine on a planet with my tech capital with 16 econ SB's along with 6 fully mined research resources and a racial research ability of 20% and that single NLC can give me 22*8*

(16*24% + 6*39% + 20%) = 2,245 RP's of research. However if I use focus to use the same NLC to generate industry, the most I can get is 22 SP/MP's of industry. Clearly this is an extreme example, but it's definitely true that if you use actual research buildings on research bonus tiles that you will be able to generate higher levels of research than by having just a bit more industry and using focus.