Why not? Balance of powers, right? If the Judiciary can't lock up the Executive, then the Executive can do whatever they like with impunity. The three branches are supposed to check each other's power.

Check each other's power - but not be in a position to prevent the other branch from functioning.

The Judiciary has the power to tell the Executive Branch that it has to follow the laws. But it can't put the Executive in prison. If the Executive needs to travel to Europe for a summit, or to Washington to give the State of the Union Address, or to the War Room to oversee defense operations, the Judiciary can't impede him from doing that.

When Clinton was being sued, the Court held that he could be subject to ordinary judicial processes - but that was based on a finding that participating in a civil suit was a sufficiently minor imposition on conducting the affairs of the Executive that it wouldn't violate separation of powers. The Court found that the Judicial function could be exercised in a way that did not impede the Executive function. But forcing the President to serve a term of confinement can't possibly meet that standard. And honestly, can't work practically - you can't have the President in a jail cell, removed from the Pentagon chain of command and the nuclear codes and everything else.

In today's world, there's literally no possible way for the President to carry out the required duties of the office if confined to a single location. Given that, I think the courts would (correctly) determine that the Judiciary is precluded from imprisoning the Executive. Especially since there is a solution that would avoid that conflict of powers: just set the start date of his sentence to after the conclusion of his term. That happens all the time in criminal proceedings - recently and notably, Elizabeth Holmes was sentenced in November and didn't start her prison term until six months later. Delaying for a few years would be longer than is usual, but also not unprecedented where circumstances call for it - using another famous person example, when the "Real Housewives" husband and wife were sentenced to tax fraud, the husband's prison term didn't start until the wife's was over (several years after trial), to avoid having them both in jail simultaneously when they had minor children.