Increase runtime: batteries in parallel -> buck || batteries in series -> boost
You say that having 24 batteries in parallel gives you an easier charging circuit and that is true but, it's also a technical compromise in that you cannot ensure charge current is balanced to all 24 parallel batteries equally. Having the batteries in series means that you can make a much better job of charge current balancing the batteries but, it does have more complication.
Therefore, my preference is &quot;series connected&quot; because it brings an improved level of security in charging the batteries. Also, a buck regulator that is used to step-down to a lower voltage, provides slightly better efficiency than using a boost regulator to step-up voltage (for the same circuit complexity). Clearly using a synchronous regulation is more efficient than using a non-synchronous circuit too (because you don't lose power in &quot;the diode&quot;).
If you decided on a parallel arrangement I would prefer to have independent parallel strings of series-connected batteries so that you could properly charge balance each cell in each string. This of course means a charge balance circuit for each cell but, it's still my preference.

Which setup will give me more runtime?

Well there won't be much difference in either I suspect so, it boils down to which set-up can produce the run-time but also, produce that run-time reliably time and time again.