It sounds like you've thought through it pretty well.
Bones: 1133, Slots: 116, Anims: 280, Attachments: 10,393, Skins: 313.
1133 is a lot of bones, but could be perfectly fine, depending on the target hardware and especially on what else you are doing in your app. If you can put bones (and constraints) in skins, they only have a performance impact when active.
116 slots doesn't say much. Vertex transforms is a better metric. Be sure to prune every single mesh, eg a max influence of 4 is common. Many tools have a hardcoded limit of 4. Avoid clipping.
280 animations and 313 skins is fine. They take up some storage and memory but otherwise have no limit or performance impact for having many, beyond loading. Avoid deform keys.
10,393 attachments is OK for the editor. As you found, the editor can scale up to around 80k. We might be able to scale farther, but honestly we don't put a lot of effort into that. You probably shouldn't rig 80k attachments in the editor as it would take an ungodly amount of effort. At that scale you definitely want to find other ways to do it.
New skins aren't just texture swaps – they have unique meshes, attachments, and even animations, so artists have to build them in Spine. Can't do it at runtime easily.
Every mesh is truly unique? Are you sure you can't use template attachments? It may be easier (now) not to, but the advantages are great. When using templates the images don't have to be the same, it's normal they have whitespace. With region attachments the whitespace doesn't take up atlas space and doesn't even use up fill rate at runtime, since it is not drawn at all -- prefer regions over meshes where possible.
Editor performance aside, needing to rig tens of thousands of attachments in Spine is very time consuming. Templates and conventions can save a LOT of time and effort, allowing artists to focus solely on generating new content. Even if you need many templates, reuse could still save you a lot.
We don't have a way to do partial skeleton exports. A single skeleton is always exported together, as fracturing it into pieces invites problems that wouldn't otherwise exist. Still, you could export and then break up the data relatively easily. If you do, I suggest doing it with the binary format. However, doing that solely to avoid loading attachment data at runtime isn't worth it IMO. 6MB memory per 10k attachments is reasonable.
Exporting the whole skeleton but only a single skin, so it can be imported back into the editor, isn't great. I think a better idea is (worst case that you can't use templates) to just copy your project, delete all the skins, then juggle 2 (or more) project files. That allows you to scale to any number of attachments, as far as editor performance is concerned.
That works OK as long as you don't change the structure (don't add new bones, slots, or constraints). At some point you probably don't want to keep adding those things anyway. If you do need to change the skeleton, you'll have to change it in all project file copies. That is the fragile part.
With multiple projects, at runtime you may be able to load multiple skeletons, then use skins/attachments from one skeleton in another. Check what references are kept to be sure, there may be some minor fix up. If you mess up and change the skeleton bones/etc things will break.