I guess the ideal is to have the handle match the leadouts (ie - since the throttle lead on the handle is short, then the throttle LEADOUT should be long -). If the handle leads match the leadouts, your lines would need to be all the same length.
In the real world, however, that would require three precision lines. It is far easier to have a set of lines that stay with the plane they were made for, as detailed on other threads. Then you can use different length line connectors to fine tune them. I actually go to the trouble of setting up each plane for a particular handle, and then marking on the wing tip WHICH handle to use with each.
It really comes down to getting the two elevation lines about the same, so that you can fly with the elevator as neutral as possible (because the handle has no way to adjust any of the lines) and getting the throttle line to move the throttle through its complete range - if it is too long or too short, you will not be able to get all the way to full throttle or all the way to full idle (one or the other).
That is why the advice is give to not mix J Roberts handles with LR/Brodak bellcranks or vice-verse - the throttle movement available from the handle does not match the movement range of the bellcrank.