Yes, I think that is the intent. Research Project works the same way: you run your production through your entire manuf bonus pipeline, divide by 4 to get Raw Research, and then run that through your entire research bonus pipeline. So all of your bonuses in both pipelines pay off.
This matters for e.g. Altarian, who have the Dark Energy branch that pump both manuf and research. They don't have to choose one or the other; they can pursue both.
It's ba-roken only at late-game levels, e.g. you researched Terraforming deep enough to turn your 10 to a 26, and researched manuf deep enough to get max manuf, and maybe destroyed and rebuilt improvements to maximize adjacency bonuses, and researched Economy enough to spam starbases. If you haven't been invaded three times over or won the game already, you deserve to profit from whatever you generate. (Conversely, if I haven't killed you already, then I deserve to receive whatever you can buy with that wealth. Or maybe I have research worlds just as sick as your wealthworlds ... and I'm turtling while I research a Technological Victory.) Even if a moneyworld does just buy a win, maybe the more efficient strategy is to do only 1/4 of that, and then go win the game much earlier ... and players who adopt that might gradually out-compete you in the open environment. (I have that problem in eCCGs, where I turtle until I'm ready, and then end up wining by ridiculous overkill ... which meant I could have won by a razor-thin hair several turns sooner. It does matter when the game is fundamentally a race.)
Expect all numbers to get tweaked many times between now, Beta 3, and Release. For example, we know Drengin improvements are underbonused, tourism is overvalued, maintenance costs are too low, and diplomatic trade agreements are whacked. In general, expect everything to get scaled to make things ... harder. That could mean it will get harder to overproduce at these scales ... or it might get easier, and every AI will do it too 
