Can you freeze homemade clam chowder?

You certainly can. Just thaw it out in plenty of time. Don't try to rush it in a microwave or anything. Then mixing well should avoid the 'watery issue'

Milk based soups can get watery after freezing but no issue with safety.

Yes, but the potatoes might suffer. If you use waxy potatoes, the texture should be ok. I think russets become mealy when frozen.

yes you can