Counterintuitively, you can raze your +research buildings in the town to reduce the negative research.

On the flip side, if you research lots of the +research tech then you can overcome the malus from Temple of Forgetting/Set in Stone, at which points the +research buildings become "profitable" again.

No it not really buggy is just arithmetic with a poorly labeled description in the spell book for “set in stone”

Both the Temple of forgetting and “set in stone” give a modifier of -100% research to the local city

If you have the scholar or educated soveren and race traits you get +10 or +20 % global reserach bonus 

Every enclave you build the lvl 4 upgrade academy of revelation gives you +10 % global reserach bonus

Everytime you reserach advanced the +reserach tech you get +10 % global reserach bonus

Thus you could overcome the -200% local reserach penalty with combined global +200% reserach bonus.

That depends entirely on how they set up multiplier stacking, and from everything I've seen in the game it appears that most percentage bonuses and maluses are additive, rather than multiplicative. This makes the actual modifier to your research (or experience, or whatever) equal to

(100 + bonus1 + ... + bonusN - malus1 - ... - malusM)%

of the base value (bonus1 to bonusN and malus1 to malusM are expressed as positive percentages, i.e. a 10% bonus is 10 and a 25% malus is 25), rather than

(base value)*(1 + total bonus expressed as a positive decimals)*(1 - total malus expressed as a positive decimals)

which would give you a system where you could not really cancel a 100% malus.