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Tell me what I'm misunderstanding here.
So I dug into the source code a bit to see how it's used. It turns out that IPFS might actually optional, as per the log line on https://github.com/hyprspace/hyprspace/blob/master/p2p/node.go#L213 ("Getting additional peers from IPFS API")
The list of required bootstrap peers is hardcoded in the same file, but a few lines above, specifically at https://github.com/hyprspace/hyprspace/blob/master/p2p/node.go#L181
I say might be because - while the required bootstrap peers include a bunch of ones based on bootstrap.libp2p.io - there is a long list of hardcoded ip addresses and I don't recognize any of them.
So those might be libp2p.io ip addresses, but they might also be IPFS ip addresses, or even belong to someone else altogether. (Edit: There are WHOIS tools online like https://lookup.icann.org/en that can be used to look these up and figure out who they belong to if you are really curious, but I can't be bothered to do that right now.)
In any case, it looks like the way this works is that from a peer, libp2p tries to look up additional peers, and so on. So at most IPFS would be used as a way to get a listing, but once the desired peer is found, IPFS is cut out of the picture for that particular connection and NAT hole punching is used to establish a direct connection between peers instead (as per the linked wikipedia article, https://en.wikipedia.org/wiki/Hole_punching_(networking )