Do Research Bonuses count in an all-Factory build?

AFAIK the boni are applied to focused research, but I guess one of the strategy-gurus like wyndstar would have a definite answer.

While at it, why do the AI persist on planting enhancing buildings (powerplants, coordinators etc) on the bonus tiles and the actual production buildings on ordinary tiles?

I've rarely seen that on the latest DA builds, though it used to be more common. The AI is using bonus tiles quite well now, from what I see.

There's always the chance that the AI built as it did based upon short-term goals, which didn't pan out in the longer term. For instance, it might use a bonus tile for a different kind of building if it thinks it absolutely needs a certain building immediately, whereas another tile isn't available at the time. That kind of "logic" is probably hard to code against, because it does have its own sort of purpose.