One way to address this problem is to acquire a lower door threshold seal unit that slides onto the bottom of the door and is adjustable by sliding up and down to the threshold. They are then fixed into place using screws through the side flanges into the lower rail of the door.
Here is a picture of what the product looks like. They are sized to the specific thickness of the door.
You would remove any existing lower door seal before installing the new seal. In some cases it may be necessary to trim the door some if the lower height requirement of the new piece is more than the current gap under the door.
You should be able to find these at most big box home stores. I saw mention of the orange one online.