Version 1 is actually more common than you think, though it's usually not just for none/something meta options (and yes, I'd argue that is a meta option since it's selecting the type of option choice, not the choice itself): many interfaces that utilize complicated options with some kind of meta-choice have a similar checkbox/combobox interaction. KeePass, for example:
Since there are several different and distinct meta-options for what kind of authentication you want to use, the checkbox helps distinguish which you intend.
The important part is getting the interactivity right: making a change to any one of the fields marks that meta-option as active. Typing in the Master Password field checks that box; selecting a Key File marks that as active; etc. This keeps the 'clicks' to the same number it would be without the checkboxes, except when the user specifically uses them. It also reduces the clicks when the user wants to select the default option under a meta-option - then it's just one click (instead of two: opening the dropdown and selecting the other option).
A major pro of this route is also that it can save "preferences" for default options per each meta-option in case the user changes their mind about which they want to use: if I type in a password but want to use the key file I just browsed for and found, it's just a single click to go back to it, as opposed to losing my choice and having to browse again (and vise versa, my typed password isn't lost when I do this).
Many more applications do this and you probably don't even think of it as a design pattern: installers often give a choice between the default install path (the 'none' checkbox) and a custom one (file browser input); or browsers that ask where the downloads folder should be vs. always asking (pretty much every browser).
The cons appear when you don't get the interactivity right: either making a change/selection in an option doesn't automatically select its meta-option (adding a step that might be overlooked or missed by inattentive users) or it clears the other meta-options' choices (as in, selecting a key file clears the password field) and penalizes users for changing their minds.