If that was their intent, then yes, that would be an issue. The key is good UX; don't send the user there without explanation. A well-designed "read this!" screen is key, and even then you will lose some users. It's a trade-off.
Also, I did acknowledge that this approach will turn away "mass market" users, but again, I don't think that those users will ever be Signal's primary user base. Most people are going to use stock apps or whatever is most heavily marketed (read: whoever spends the most dollars on acquiring users). Signal frankly can't afford to buy its way into the mass market. It's a niche app, and it should focus on catering to that niche.
I read
> 2. The user hasn't installed the plugin. Who does that? So signal doesn't work.
as "when the user sees that it doesn't work out of the box, and sends you to an app store instead, they consider it broken."