My belief is that a longer stroke crankshaft enables the huge benefits of being able to select the power characteristics of any cylinder kit. Essentially, far from your assumption, a longer stroke can mean that exhaust duration can be lowered, thus making an engine far more tractable.
Much depends upon the whole package & having an understanding of what each part of the engine contributes to the overall performance.
The trouble with all of the available knowledge concerning tuning is that there are contradictions & that makes selection difficult unless you gain some understanding of how things work.
For instance, there are marvellous looking HPC crankshafts that are fully balanced, but I am of the opinion that Lambretta engines need a lower primary compression to yield benefits. Consequently, the longest conrod available is also my automatic choice, along with a longer stroke. Following that logic, enlarging the transfer ports in crankcase & cylinder may not be 'fashionable' currently, but I believe that it benefits the delivery of the fresh charge to the top end in a controlled manner. Instead of high pressure squirts into the upper cylinder, lower pressure transfer means that the fresh charge is likely to be less mixed up with the escaping exhaust gases & yield more power. That logic is nothing new. The Japanese etc have been producing engines with low primary compression & large transfer port area for decades.
The last engine I built gave me the opportunity to be the most radical I have ever been in applying my preferences, even though it was not my own engine......nice to have that trust
Even though that engine has not gone near a dyno, I know it works really well with more to come. The next job is to make or modify an expansion chamber to suit. Volume is the issue so a large mid section diameter is fundamental along with a manifold that is angled downwards.....