Hey there,
it's been a while since I wrote this extensions for someone on reddit, so please excuse any misremembered facts on my part.

"Access your data for all websites" was iirc a requirement for the JS-alert. As the default Firefox notification is displayed only for a short time, I wanted a way to make sure the user interacts with the alert, as a way to make a conscious decision to either stand up or ignore the alert. However, to inject the JS into the webpage, the aforementioned permission is required. Not the way I wanted to do it, but I wasn't able to find a better solution at the time.

Regarding the icon - it was a decision I made back then because I felt like the addon doesn't require an extra icon. I thought it quite likely that a user would want to set the timer once, and then only wants to interact with the reminders. Having an extra icon in the toolbar would have been an annoyance (to me). Instead, user input relies on the 'options' tab of the addon manager page, which, due to recent changes to the addon manager, it no longer as visible as it used to be. I might have to rework that when I have some time, that's true.