Thank you for considering it, as it's still an ongoing issue for me.

I have added this request to the tracker:
Issue 2217 – Make it harder to mis-click "never show this again" checkboxes
You can vote for it there.

Thanks for your feedback.
I'll think about it.
Note that the space is already used for additional protocol options and notes. We would have to make the minimal height of the Login dialog higher.
And the current placement of the checkbox is consistent with "Never ask me again" checkboxes on some prompts.

In a future update, would it be possible for you to move the "Show login dialog on startup and when the last session was closed" option from below the "Login" and "Close" button to above them?

I am mis-clicking the Login button – which is unchecking that option without me realizing it – and requiring me to hunt down the option to re-enable it the next time I load the program.