Regarding the practical implications for a science fort, do all the mechanics imply that it is much better to make separate libraries for different academic areas?
You are correct that scholars only discuss with scholar sharing their library. In addition, discussing only takes one day while pondering takes two. So I think you are right, specialty libraries focused on separate skill areas makes sense. I would add that you should give skilled researchers their own separate libraries, and then give them an unskilled dwarf to work with. The unskilled dwarf will gain skill from discussing with them, discussing awards more XP than pondering (10-30xp for discussing versus 5 xp for pondering according to therahedwig's tests). Also, even if the skilled dwarf wastes on average half their time discussing the unskilled dwarf's topic instead of having the unskilled dwarf discuss their topic that will still not add any time to getting research done because discussing only takes 1 day while pondering takes 2.
For training scholars from 0xp, note that several topics actually use skills that have practical use and that can be trained other ways, in particular a bunch of engineering topics use mechanics, many medical topics using surgery or diagnostician, one topic uses organizer, and a few topics use record keeper. So you could have mechanics churn out a bunch of gears to grind their skill before setting them to do research. And you could rotate out noble assignment of manager and chief medical dwarf to scholars.
Did they switch topics?
They were pondering the same thing (path of the moon I think? I can check tonight) according to the in game labor description and the dfHack script output looked the same as before they earned research credit.
Edit: checking through again tonight... I've got a dabbling logician that got 800 research credit after 71-72 times pondering. So the base level of research credit isn't 1000, it's just that the skill roll for even unskilled dwarfs adds a much larger amount than the base value of 100. Also, I checked and my astronomer is still pondering the same thing and still at 0 research credits, so somehow research credit can go down or dfHack is reading it wrong...
Edit 2: Proficient Chemist is up to 15200 from 9500, an increase of 5700, after 50-60 times pondering. Skilled Optics engineer is up to 8400 from 5600, an increase of 2800.
Edit 3: Competent Astronomer, that had previously been set back to 0 by some glitch or undocumented feature, is now at 3100 (52-60 times pondering).
Edit 4: Proficient Mathematician, up to 15300 from 9700, an increase of 5600, after 60-70 times pondering.
Edit 5: Competent Astronomer is up to 5900 from 3100, an increase of 2800. Novice Logician is up to 2500 from 800, an increase of 1700.
Edit 6: Skilled Optics Engineer up to 12100 from 8400, an increase of 3700.
Edit 7: Talented Chemist is down to 0 from 15200, still pondering the same topic (Hardness). I think it is important determining if this is a bug in the script or a bug in the game or if Toady missed describing something important.
Edit 8: Talented Mathematician up to 19200 from 15300, an increase of 3900.