The clones are at the exact same stage in life as the mother. Autoflowers don't ever stop flowering. So you can't clone them. Which is why a lot of people suggest you not bother with them indoors.
That said there is utility to them in some situations and making seeds is fairly easy. The problem with seeds is that it is highly unlikely you will get great stability from them unless the line is heavily worked. And if a line is heavily worked then you run the risk of inbreeding depression.
F1 hybrids are what most growers really want in their garden. Whether they know it or not. If you make seeds of a true F1 the progeny will be extremely unstable, even if the F1 was very stable (real F1's are very very stable unlike the myths about them you see thrown about in the cannabis community with people routinely claiming they are not - actual F1's always are. Polyhybrids which are not actual F1's are not - at least in the real plant breeding community that does it professionally for things like tomatoes - which by the way it takes about 15 years to stabilize a new variety).
Despite clones not being very useful for general use (in autos), they can be useful when you're breeding. Especially if you're breeding for female seeds. I won't get into details as to the why I think I've addressed your main concern.