I went through the same worries, in hindsight I would say don't worry about the fact it there are "sumps" in the system.
I have the same kind of plumbing conundrum. In the last decade / 1,100 hours of operation, it's caused exactly zero issues or worries.
You do have to be careful about fuel lines moving as everything "settles" once you start flying, anywhere a fuel line could rub against any other part - including the tunnel or boot cowl - you need protective rubber or plastic covers over the line, ideally with some red RTV for good measure (AKA anti-chaffing compound

).
If you are focused on flow rate, I think the only time it matters is with a constricted system with too many fittings, then a flow rate problem can occur and this has happened a bunch of times for different builders. Typically with an O-540 carb engine, with a lot of extra fittings and trimmings, fuel filter, flow transducer, pump, etc in the line causing pressure losses which reduces flow rate. Otherwise I don't think it's a problem, especially if you stick with Bob's fuel system design per the "Bearhawk Book" or whatever might have replaced that guidance.
If you are going fuel transducer, you can leave out the flexible line if you like. It doesn't seem to cause any issues, I know several aircraft which have them in line with hard-lines only. Sometimes people do have issues with occasional high readings, intermittently, but I don't know of anyone who's found that flexible tubing resolves that issue.