In the spaces where waves and wakes make a difference the tolerances are larger. The one exception is for example smaller commuter ferries without a ramp, then you might have to time it as you say.
Wind and current doesn't really matter as long as you have dynamic position which abstracts it away as long as you keep within your power budget. The real hard part here is moving through a shifting environment, for example the current often reverses along banks. Especially in a river based harbor environment where you've created piers and what not disrupting the flow.
In a previous life I worked as a skipper in just those conditions, passenger ferries in the 25-40m sizes with a couple of hundred passengers in river harbour environment. Two props and bowthruster and you have to keep all the considerations you mention in account. Especially since you can't angle the stern without angling the bow (duh) when you're applying reverse thrust to dock. And with some speed forward you move the center of rotation forward making the bow thruster less effective.
It was actually easier with quite a strong wind since then that would overcome the current easily and you would lie on the wind margin side of things. If you come too high just make the docking take a bit longer so you would blow down and land perfectly. In almost calm conditions you would instead have to guess which would win that time, wind or current.
That said, the ones with two pods, one at each end you just balance things out and go straight to the dock.
