All evaluation (of civics, buildings, etc.) is necessarily generic (i.e. - it knows nothing about specific buildings or civics at the code level - only what it reads as their properties), so it may be hat it undervalues buildings enabled by techs. I'll perhaps consider tweaking that up a bit.
Edit - I just had a quick look at the building evaluation code in the tech evaluation (i.e. - evaluation of buildings the tech enables), as it's not code I was familiar with (it's quite separate from the building evaluation code that cities use, which seems a bit weird in itself!). Anyway, it turns out that it only does a VERY cursorary job of evaluating buildings in that context, and science bonuses are totally ignored!
This definately needs changing, and I intend to scrap the current routine entirely and use the city building evaluator (the capital city can act as a proxy for most purposes), which is FAR more complete. However, this is a fairly major renovation, so it will wait until after the next release, as it might have unintended side effects until bedded in.