The limitless options for koma is confusing, but remember that none of it really matters. The same thing happens in the coffee world, tech world or perhaps anything that can be customized - I.e, when the user pursues more variety, greater-than-necessary importance can get taken into it. For example, a techie can get passionate about a processor being 1ms faster/slower than another and hyping that difference. Likewise, some people in the shamisen world get very passionate about the tone change of a koma 1mm wider/thinner than another. It’s true, there is technically a difference in tone, but it’s so minuscule that it’s far more beneficial to put that focus into actually playing the instrument. 
Playing with different materials is fun, and it’s great to try them out. But always remember that if one focuses their energy towards playing, far more tonal improvements will be noticed regardless of equipment. As an example, here’s a video of Nitta san using a plastic bachi. A hard plastic bachi is not pleasant to use, yet Nitta san has so much playing experience, he can make it sound like a dream bachi.
True. Unless you are studying under a teacher and want to learn a specific style, you can usually use any koma for any shamisen. 
When I give shamisen group workshops, I use nagauta shamisen outfitted with tsugaru koma. They sound just fine. A taller koma would sound different, but not better or worse. Without a teacher, personal preference is the biggest deciding factor, I believe.
The Deluxe koma is sized for the dou of a tsugaru shamisen, but personally, I’d trim it down to fit the nagauta shamisen, and use a file to make narrower string notches, if need be. 
Ah yes, professional nagauta shamisen players like to reskin their shamisen a LOT. Personally, I think it’s a bit too neurotic. A friend of mine (who reskins shamisen) gets a bit irritated with them because after one concert, they’ll take their shamisen to be reskinned before the next concert the following day. What’s more, they always want their shamisen skin to be even tighter than before. “Cat skin can only be tightened so much. The skin was already so tight, why change it?” he asks. For the skinners, it feels like a waste of skin. They know it’s a good skin and it’s tight, but the player is so absorbed in their own aesthetic, what they think is better.
These nagauta players probably change their skins once a week (if not more), whereas Nitta san (who is one of the highest-level shamisen players in Sapporo) changes his skin about once a year. Similarly, his koma is bamboo with a little sliver of bone on top. Two professional players with polar opposite aesthetics. From these examples, I feel high aesthetic standards seem to be a judge of a player’s ego more than their skill.
That’s why I prefer to downplay the importance of aesthetics, because it seems based in the mind more than in reality. Thus, we’re just keeping our koma selection simple and refining it to two options, one for a brighter tone and another for a warmer tone. Nitta san’s favorite koma is bamboo with a sliver of bone on top. If that’s good enough for him, than it’s should be good enough for anyone else.
Note, this is all personal opinion.
