How would people's unread replies, subscriptions and bookmarks be able to be made fully compatible {seamless} with the "chaining" threads function?
Not sure what what you mean here, but I think I'll answer below.
In other words, would they be auto-subscribed to new ones? How would we avoid piling up on 20 or 100 chain-links of a very long-running topic?
What of all the manually created links to threads that use the "#new" function to bring the clicker to the first new post in that linked thread? Would it carry through on treating the newly created "chained" threads as part of this link, or would it die? This is a must for us because we have events that are linked to and that in their peak will generate over 6,000 posts in a day.
SMF's original behaviour is not changed.
You can surf pages like normal: you want to go to page 6 of a topic? You can, once you are *inside* the topic starting from that page, the trick will load the subsequent pages at the end of the current one.
Let's do an example: you have a 20 pages topic.
You go to page 1, scroll down, it will load page 2, scroll down, it will load page 3 and so one.
Same topic, you click a link that brings you to page 15 you are normally brought to page 15, scroll down, it will load page 16, scroll down it will load page 17 and so on.
Same topic you have read it all in the past, a new post comes up and you click on the "new" button, you will go to the first unread topic directly (like with a normal SMF installation), if this post in the last page than the trick will not load anything else, if the post is no more in the last page, the scrolling down it will load the last page.
We have an upcoming groups feature being created that will place threads in groups too, and I am wondering if it'd be possible to auto-subscribe these chained threads.
Not having any idea of how this works, I don't have any idea if the two will work properly together...
Probably these are not concerns for smaller forums, but when you get to my size, suddenly a lot of things that were never issues before become issues, sometimes big issues. 
We have a lot of issues related to thread lengths and profiles with large numbers of posts on them, in general. It seems that when a forum reaches large size, you get a lot more members with huge numbers of posts and also threads with obscene numbers of posts, commonly you get threads and profiles with 5 and 6 figures.
Of course I have no idea of how this is scalable in the real world, though it should not load the server more than the normal view of a topic from a user (since in fact it doesn't do anything else than load the "following" page by javascript and inject it in the current page. Of course if a user goes through a 2000 pages topic all by this means his browser will most likely crash due to memory usage I'd guess.
ETA: one possible annoyance could be that someone could start from the first page of a topic, push the "end" button on the keyboard and make all the topic load (almost) without interruption. That could increase the server load.
Note to self: add a minimum time before load the subsequent page.
