Player options are rarely for the team's benefit. They're designed for the player to get money the team doesn't want them to get. Often, that manifests itself in bad players opting in, like RJ did a couple of seasons ago. Philosophically, though they are injury insurance, like Gerald Henderson picking up his option this year. If Tim and Manu wanted to be one and done, then a one-year deal makes the most sense. If they wanted to go one-and-one, then a one-year STILL made more sense, as it would have allowed both sides to maintain flexibility.
So why did they sign a one-and-one deal? It was because they were undecided on coming back, but I believe the contingencies are the opposite of what you'd expect. If the oldies come back next year, I expect them to opt out, as it would allow for the team to potentially pursue a max free agent or failing that would allow for the Spurs to use their Bird rights to give both guys a nice send-off contract. If they plan to retire, on the other hand, they'll take the money owed to them, which the Spurs would gladly give, seeing as both guys got under-market value on their deals to allow the team to sign LMA.
I will reiterate that you are correct that it could work out that the opt out to retire or opt in to return. But the former situation is too good to hope for, while the latter would be inefficient. Opting out is better in any scenario in which the Spurs wouldn't try to force Manu or Tim to retire against their wills, which I think is a safe bet to not be the case.