FFS, no community mods are going to be "integrated" into SS2EE. It's going to have a built in general-purpose mod manager, and some community mods will be included (i.e. pre-downloaded) by default.
Presumably the description for each mod will also include where to go to check for updates, which puts players in no different a situation than if they downloaded the mods themselves. It's always been up to the individual to keep on top of updates.
You severely overestimate the intelligence of gamers.
If they weren't already playing the standard version using ss2tool, there's little chance they are going to bother to read changelogs, look for updates, or go mod-hunting. As far as the average player will be concerned, they will go into the mod manager, tick some boxes, and hit play. If something breaks with one of the mods they will blame nightdive. If one of the mods gets out of date they won't update it.
(Stupid) people want their games to "just work" with no effort, reading or fiddling.
You're correct in that, from a technical perspective, a mod manager with included mods is essentially the same as what we have now, with a few steps removed. The issue is one of perception. Instead of being a community mod manager where all mods are downloaded individually, this will instead be seen as "official", which means people will have the expectation that they can simply enable what they want based on a brief glance of the description, and expect it to work forever, because Night Dive is expected to look after everything. Even if nightdive was to plaster a huge red banner at the top of the mod manager saying "PLEASE READ DESCRIPTIONS AND UPDATE AS NECESSARY", people are still going to treat it as if it should all just magically work.
As someone who puts a significant amount of effort into my work, and who also provides a donation link on my website, I'm really not interested in a bunch of people acquiring my mod elsewhere, not reading the readme, and thinking it's actually nightdives work (or, at least, some nebulus "community" mod attributed to nobody in particular). Especially if it also takes attention away from the excellent community mods on the forum, encouraging people to only play the "blessed" mods. If the randomiser was included, for instance, I'd really want people to play it with rsd since, while it works perfectly fine with vanilla and SCP, I feel the item distribution is better overall with rsd's item rebalance.
I'm probably overexaggerating here, I'm basing this off the general modder drama from when the Nexus added collections, which for the most part took attention away from the original creators and encouraged people to download from (and tip!) the collection creators instead, which was a major backwards step for everyone. Mod makers hated it because it took recognition (and money) away from them, and would result in a lot more false bug reports when the collection maintainer screwed up and broke their mod, usually by including an incompatible mod.
This is all largely moot anyway though, since nightdive has not asked to include any of my mods in SS2:EE, nor do I expect them to ever be interested in doing so, and I didn't intend for this thread to become a discussion on included mods vs manually downloading them.