Yeah, the installer launches your default browser upon completion. I agree that it's super weird, but it's an intractable problem in the current design. It seems like there was a historical assumption made that "normal" people use one browser, and that it's default. As you've observed, that was a pretty naive assumption.
On the bright side, our distribution team is actively working on a new installer (this is one of those big company things where we're using centralized technology from another part of the company), which we hope will resolve this.
In terms of the always allow updates dialog, I'll take the feedback to the distribution team. There's really no ulterior motive there. It's a herd-immunity thing. The faster we can protect you from exploits in the wild, the less profitable and useful they are for the entities that sponsor exploit development.
While we do occasionally break things (some security changes get pretty invasive), we try to keep the maintenance releases that we push through the background update service restricted to just security fixes and critical customer issues (things that have come up in the field from the prior major release, fixing problems introduced by new browser or OS changes, support for new GPUs and display technology, etc). The major feature-bearing updates are going to prompt you to do a manual download anyway, so you do maintain control over the riskier upgrades even when opted in to automatic updates.
Your point is well-taken about respecting the originally selected preference though. That said, I'd really encourage you to consider taking the automatic update path -- especially when servicing your less technical friends and family. You're doing them a big service by steering them towards either automatic updates, or one of the browsers that bundles Flash Player directly, like Google Chrome or IE on Win8+, where updates are done in-line with either Chrome's updater or Windows Update respectively, where there's nothing to install or maintain beyond the initial browser installation.
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