I'll take one item at a time.
You mention "natural" cell size in your explanation, and I guess this also is connected to your choice to go with smallcell.
Forcing bees on smallcell, is NOT natural.
Natural drawn comb has a wide range of cell sizes dictated by the bees needs, time of season, use of the cells within the hive, etc. There are maps that even show based on elevation and geographic area, bees will build cells differently based on this criteria.
I'm not against smallcell. But I am against the idea that smallcell is "natural", "more natural than this or that", or any suggestions that this is what bees would make if it were not for the beekeeper forcing them onto bigger cell foundation. Bees will not regress themselves completely down to or below 4.9 no matter how many times they have the chance. People who keep TBH's, and natural comb frames can see this.
You ask about "why" bees were on larger cells to start with. You must go back to a time when winter loss was almost 0% for all beekeepers. A time when t-mites, v-mites, and other problems did not exist. There were seen advantages to having larger bees, from nectar collection to hive synergies in less wax used for comb making, to cluster nest, etc. And if it were not for the many man-introduced problems, we would probably not be having these discussions. There were AFB (a big problem) and other issues, but nothing that created winter loss or hives crashing as we have recently seen. I don't see the cell size as damaging as the introduced problems we have inflicted upon ourselves, which is completely unnatural in all aspects of what nature dictates.
I am glad to see that you are doing a multitude of items and tackling this as an overall IPM program. For too long, I have heard claims that all you need to do was regress down to smallcell, and seemingly every problem known to beekeeping would go away. I have smallcell, natural cell, and regular cell hives. It is a complete IPM program that gets the best results no matter what comb you use.
Ok, maybe two items....
This whole swarming issue is always interesting. As with many things, I think that breeding out one trait may actually work against another trait you may want. Do we breed out swarming, and have less complacent bees, willing to overlook the need to replace a queen? Swarming is a type of supercedure. We know that studies have shown that first year queens coming out of winter swarm half as much as a second year queen. We also know that a first year queen on average, will produce more eggs, and the colony will produce more honey. So perhaps, understanding what nature dictates and has shown us in what is advantageous is something we should build off of.
I think much of swarming is dictated by flows and urges that are not so easily changed. Yeah, I have heard that this swarming thing has been "controlled' so to speak, time and time again. And 100 years of breeding later, I would suggest were not far from where they started. To me much of it is hype, and marketing to an industry.
Nature gave bees many advantages for survival. So what's next? Russian's shut down in a dearth...are we to change that? Russians go through winter with a smaller cluster... are we to change that? Each of these traits are an advantage, and an item to understand how, and why, the Russians do some of the things they do. And overcoming mites, is easier when you understand how fresh queens, brood breaks, and overwintering ability, all come into play.
99% of swarming control to me is dictated by beekeeper influence. I think you will be dissappointed if you rely on some notion that you are getting a non-swarming bee line from some breeder. You would be better off understanding how to suppress, how to control, and how to use these traits to your advantage. Simple skills such as removing the queen half way through the flow will not only allow you to control your bees and build your colonies, but will allow you to harvest more honey. (which are management skills few use, because the average beekeeper does not understand these skills and does nothing for swarm control except putting out traps and then complaining that their bees swarmed.