

I checked: definitely the first one. Also another check: blocking does work to not show the comments, I checked both blocking all users on a particular instance and blocking a specific community, and in both situations those comments did not appear, though all the other comments did.
I can see how for some people it could be a good idea to switch to the second though, e.g. in the form of allowing a toggle, and yet allowing all also does facilitate community discovery, at the expense of exposure to less well moderated areas of the Threadiverse. Although I’m personally really enjoying seeing comments from communities that I choose to not appear in my Subscribed feed on the main page, so I would hate for your second way to become the default with no option to change it.
Overall I feel like the addition of this feature, while not perfect (your point about it being opt-out) is more of a “10 steps forward, half a step back” kind of thing, i.e. the advantages greatly outweigh the disadvantages, even though the true ideal would be to put the choice into the hands of the end-user, as PieFed does so exceedingly much of in so many ways, yet this feature is so very brand-new so not this one currently.
Edit: ultimately, the way it is now, the choice of which ones to show is primarily in the hands of the OP, who chose what communities to post the link to. Plus also if anyone else cross-posted it. A PieFed user can override that decision, but only by either blocking or ignoring (scrolling past) the comments that they do not want to see. This makes sense to me.
Unfortunately, the former is rather what should be the case, although so many times it is not:-(.