For context, I've spent the last 2 months working on an extension that asks users to install from our site during signup. Making them install through the Web Store will increase confusion (why am I no longer on CoolWebsite.com?) and hurt conversion rates.
That should address any user confusion, while still hosting the extension in the WebStore. It also saves the hosting bandwidth and guarantees that your extension updates over a pinned SSL channel, which protects your users in case your key is ever compromised.
will it really? do you have any metrics or research that backs that claim up?
I would have hoped that users would be more trusting of an installer from a vetted source like the app store than they would be of an unfamiliar file extension from an unknown website.
Still, it makes me nervous to be building a startup around a platform that can make such major changes so quickly.