Yes, obviously only one sprocket can have perfect, zero deflection, chainline. So in multiple gearing, perfect chainline is less of an issue than it would be in SS. But still wand decent cheniline to keep the deflections minimized.

You have two basic choices. Set the chainline so the maximum deflection in either direction is minimized. Or offset the chainline slightly to either side of the cassette for better chainline in the gears you use the most, accepting that the maximum deflection in the other direction is worse. This is how I set up my bikes, offsetting slightly to the outer half of the cassette where I do 90% of my riding.

BTW- 10s chainline in the extremes is no worse than 9s, since the cassette width is the same. It's also only slightly worse than what would be used in a 2x10 setup, since the middle ring is between where either of the 2x rings are, so all gears are usable.