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It makes a difference in that you have to play perpetual whack-a-mole not only with VPN's but with hosting servers.
That is true for both cases as well. One thign to add though is that signals own cencorship circumvention makes it even better at resisting this kind of blockage then an arbitrary decentralized protocol, though for an objective comparison it would take some research.
I wasn't just talking about blockage but also servers being taken down physically or via ISP. I don't think I'm nearly as well versed in Signal as you are to go into depth of how it circumvents blockage via protocols but I assume they don't decentralize their hosts.
Signal Servers are using AWS and are spread throught the world. The entire protocl is build to remove any need for trust in those servers, so they migth as well be places in the datacenter of the NSA. So in the end it will be the same result. With decentralized protocls like Matrix you may get lucky and not have your small server taken down because it only hosts a few users, but if we are using the number of users as a metric, Signal would fare better against server takedowns, since all users are replicated throght the world, while my matrix server is the only place where my user data is stored. Then again both can deal fairly well against takedown ins single countries.