Considering installing this, do the manifolds always ensure equal flow between the outputs.

Example: 1000/s input, with 4 outputs. Will that ensure that all 4 lines will get 250/s flow (assuming all outputs are unrestricted), or do we still see some differences depending on the proximity to the input like you would with a normal pipe?

If your output paths are of different lengths (more segments in some paths), then you will see less flow rates down those paths. The starting height at the manifold will be similar to all outputs, so the difference in flow rate is because of the different path lengths.

When all path lengths are identical, there is a very slight difference that comes about 'rotationally' as the game engine distributes fluid out of each outlet, lowering the fluid height along the way. This occurs within each tick, and the difference should only really be noticeable at the extremes of flow rates / flow distribution.