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It's not that they have less speed, it's that they have less acceleration. As efficiency rises, you get the same amount of thrust for less fuel spent.
You don't actually start losing speed until you dip well under the point of optimal efficiency.
This makes balancing around that point at maximum speed dirt easy actually.
You let your ship make a short run unfettered, where you measure its top speed.
Then you take it back into dry-dock, and limit its fuel and oxidizer intake with pumps controlled by a combinator-latch. The latch is configured to set and block the pumps when the platform's reported speed V reaches that maximum value you observed. And it is configured to reset and unblock the pumps when the platform has dipped ~10 km/h below that.
The net result is that your platforms in orbit fill up the engines to full on fuel and oxidizer, which allows a quick burst of maximum thrust and acceleration to reach cruising speed, after which they slip into being efficiency throttled by having their supply come in bursts.
My mid-game 340 ton platform responsible for cargo hauling between the inner planets spends about 5k fuel for the Vulcanus-Nauvis trip at 225~230 km/h with 5 normal quality engines.
My mid game ship can go constantly with speed +/-300 between planets without any pause. Granted i use 5 rare thrusters and 8 rare chemplants (2 for water, 3 for fuel and oxy each). It is basically good for constant motion therefore it doesn't slow down loading and unloading, which is pretty great for Gleba (and you know, that feel good of a successful design).
The sweet spot is 40~45%, actually.
You can check the graph in Factoriopedia.
Fuel is cheap. Ammo is cheap. Having your platform torn apart by hundreds of asteroids spawning in from nowhere is also cheap, but in a different way.
The 'best' setting depends on the purpose. The OP didn't ask for the 'best' nor specify a purpose. Rather the question is what setting you, presumably as in individual player in your own game, and how you balance the efficiency vs. the speed.
There are, indeed, several target settings, with different results, which are worth knowing. The 75% cut-off where thrust is maximized is the speed choice. The 'sweet spot' from the Factoriopedia of 40-45% sacrifices some speed for total cost of operation. Using very little, as in the <10% range, trades speed for safety and/or harvesting ability. Others may have there own targets, and reasons.
Though my curiosity is less than the OP's, I didn't bother making a post and they did, I too would like reading what and why, or when, different players have chosen different settings. At least, for those who have chosen a setting. There's probably many who just 'build' it and don't even bother trying to target any numbers - if it gets there it's all good.
https://forums.factorio.com/viewtopic.php?t=118009
You're welcome.