Which HR zone is a 50-minute base run supposed to be in?

Well, it doesn't depend on the length but on the objective of the workout. 

For a base workout (which is the objective here), you should have the vast majority of your time in the lower half of zone 2. With 50mn length, since you seem to run marathons, I wouldn't expect much HR drift towards zone 3, but it is possible and OK. If you finish past zone 3, your pace is too fast for a base workout, or your HR zones are off.

As you probably have read elsewhere on this forum, the targets for DSW are computed as a % of VO2 Max, not based on the heart rate zones you have set up.

If the pace target is too high, it is either because your VO2 Max is too high, or there is a bias in your HR/pace relationship that leads to a wrong pace target. If the HR target is OK. then there is a bias. if the HR target is too high also, you know your VO2 max estimate is too high.

Too high a VO2 max estimate most often stems from a wrong HR Max value and/or, again, from a bias in your HR Pace relationship.

To avoid a bias, make sure you have a balanced training focus/plan, exposing the watch to a variety of pace/HR/duration intervals. If the bias persists and/or the targets are still off, make sure to perform maximal effort intervals instead of DSW targets for threshold, anaerobic and sprint workouts.

As usually, a very complete, competent, and detailed answer from Etupes25. I would only add that if you do not use a HRM chest strap, the metrics may be skewed due to the limitations of the optical wrist HR sensor. So if you do not use any HRM chest strap, definitely consider buying one.

Do you know what your "true" MHR is?

It may be higher than you think.

Thanks for your comment. I do use the HRM Pro chest strap.