If any of the guards from Theobald's palace are making it all the way to the police station, then you were doing something highly unusual and probably naughty. =)

"I meant the two more guards in the T palace courtyard (standing next to the side door) - initially they weren't there."

This is probably due to guards coming outside during a search for you, or possibly falling off their balconies during a search, then not being able to find their way back inside. I promise no extra guards spawn in at a later time.

"I believe now the same or similar phenomenon (seemingly safe by the dark light gem but actually not) may be also behind at least one or...

Definitely fair, the readables were literally afterthoughts....

The AI settings have not been changed at all. That hyper-aware behavior is due to them fully seeing/chasing the player (alert level 3). After that happens they will go back to patrolling, but they will still be at a higher alert state for a long time.

Thus you see them patrolling normally and try to come up behind them, but they might spin around ("eyes in the back of their heads" syndrome). When the guards are in this state, they will not be fully back to normal (alert level 0) until y...

There IS a way (that does not require a vine arrow) to get back across the poisoned water from inside the Keeper sanctuary, but the Keepers have the lever pretty well hidden.

It took less than a year. I've been thinking about and planning this mission since 2005, so that probably helped.