Giving advantages to the better participants is a practice common across a variety of racing sports. The idea being that, if you could earn an advantage by doing worse, then in a race where you know at a certain point that you can't medal anyway, it would be optimal to just intentionally slow down to try to come in last and secure an advantage in the next race.
As a counterpoint, think about the balancing act of trying to place as well as you can in the semifinals while not over-exhausting yourself to the point where you've got no energy left for the final.
I think this dynamic is way more interesting than what you'd get if semifinal rankings had no impact ; that latter scenario would basically result in a Dutch auction on effort, and likely suppress performance on the qualifying races.
Let’s consider auto sport. For most races, there are fixed starting positions that are determined by qualifying. Qualification is generally done by racing around the track as fast as you can without any other racer on the track or blocking you. The faster you qualify, the better your starting position. The better your starting position, the more advantage you have in the main race. If you are trying to figure out who the better racer is, it’s not a bad system. Everyone is incentivized to do as well as they can at each step.
But, I think there is another motivation to consider. I don’t think the point is necessarily to find the best racer (or swimmer in your case). Instead, I think the point may be to make it so that the best swimmers can swim their best race. The goal isn’t just to see who can win, but to see if the winners can beat a larger record. You want the best racers to have the best chance at performing their best. When the best swimmers are in the middle lanes, they have the best conditions for breaking other records.
It’s not the most fair system. Track is probably a little better, but even then, the lane you are in has certain advantages and disadvantages.
You could make it based on past performance at a given level. So your position in a qualifying race depends on your placement in last year's qualifying race. Your position at the final Olympic event depends on your placement at the same event in the last Olympics.
If it's your first time at a given event, I guess keep whatever we do now or make it random. The reason for this system would be to make surprise wins from less-known people more likely, which I'd think would be desirable.
I've heard this said before, and I understand the reasoning, but I don't think it's good enough. We should be aiming for equality at the start of a race, not giving the better people a head start. If qualifying races are broken in the way, then just randomize the starting order. Literally do a random draw as people are walking/driving up to the start. It would make the events far more interesting as well.