HTupolev

Depends. One of the differences between "endurance" road bikes and "aero" road bikes is that the "aero" bikes are on average built for a more forward and low fit. But what impact this has depends on the rider and their body geometry. If you can easily achieve the bike fit you want on either, then this isn't particularly impactful.
Sometimes "endurance" road bikes are designed to feature more compliance, or fit bigger tires to facilitate a smoother ride or to handle stuff like gravel better. If you're riding on rougher roads and this is an issue for you, then this can be a disadvantage for the aero bike. But this really just depends on the bike and the use case. Not all aero bikes offer a harsh ride, and for some people and use cases it won't matter either way.

There aren't really clear defining lines between what an "aero bike" and an "endurance bike" is, and any comfort differences that they may or may not have will depend on the rider and the riding.