Are you sure about that? The Merlin engine Falcon 9 uses has the highest thrust-to-weight ratio of any rocket engine currently being used, more than double that of the much more powerful RD-180 used on the Atlas V. You'll lose some advantage because structural support and plumbing for more engines is heavier, but I'd expect they'll still come out ahead. The Raptor has been downsized from the original plans, and Musk has said that was to improve thrust-to-weight ratio.
Why? I can't think of any reason why more powerful engines would fundamentally be more weight-efficient.
As I understand it, the main driver of scale is that the combustion chamber has an optimal size. Too small and you get incomplete mixing, too large and you get instabilities.
That wrong. They tried this on the Falcon 9, not the Falcon 9.
Re-usability was their goal early on and and it was just a question of how to get there. Its not an accident. You could of course claim the exact architecture they have is an accident. But then again had they developed this larger engine they might have moved to a larger vehicle with 5 of those before going to a fully reusable Starship style vehicle.
The important point is consistently worked towards a known goal.
The original plan for recovering the F9 first stage was to use parachutes and this was tried with the first couple of launches, but the boosters broke up on re-entry. That’s when the idea of a re-entry burn came up, and from that the concept of a propulsive landing.
But propulsive landing is only possible with the F9 because it has a central engine and the engines are small enough to throttle down low enough to do a suicide burn. You have to have an engine at or very close to the centre of the vehicle for it to work. But this 9 engine cluster with a central engine was not originally designed with propulsive landing in mind. It was an accident.
If SpaceX had better funding early on, they probably would have developed a larger main engine for the booster, which wouldn’t have been able to throttle low enough to stick a landing and may not have had a cluster arrangement with a central engine anyway. This is also why the other rocket companies mostly can’t adapt their rockets for reusability easily.