It's labour-intensive to stratify in the fridge, and the results aren't as good. Natural stratification is by far the best option. The deep-freeze doesn't usually kill things -- if anything it's like a pre-selector for the most vigorous seeds.
I do for some crops it simply because it's easy to keep track of things, but I had good luck stratifying quince,
apple, lupin, hollyhock, wingnut, walnut, oak, chestnut, Hibiscus syriacus, and other seeds outdoors. I just cleared a garden plot for them, labelled it, and they come up when they know it's time, rather than after some sort of predestined interval. I've had an incredibly high success rate with direct fall sowing, and no damping off or seedling loss. They are very vigorous.
As far as direct fall sowing in pots: I am still waiting on my Paw Paw and Persimmon trees, but I think they'll come. I did have some problems with this method because I had sown them out on a balcony, and a
mouse came in and dug up all of the cherries, plums, and nectarines I had planted. I was livid, but I know the little bugger just saw it as a winter buffet. THAT is the danger of direct-sowing otdoors without covering.
In the fridge, I stratified things like lavender and asparagus, because I sow them in individual pots with herbs and vegetables come spring. It's really just a matter of how you will be raising things as to what will be the most convenient, but there are a lot of fungal and disease problems associated with that are normally taken care of by the biodynamic ecosystem outdoors, that doesn't allow things like fungus to take over.
I'd say the reason most people are reluctant to direct-sow is because most people don't know what the seedlings will look like or how to tell them apart from the newly-emerging weeds. Maybe it's a good idea to try is indoors the first time, take a photo of the seedling, and then play around with direct-sowing the following year once you know what you will be looking for.
It's really all a matter of
experience. Stratification in the fridge is attractive for newer gardeners because it allows the maximum amount of control with the minimum amount f knowledge. It takes time to build up a memory bank of what seedlings look like, especially when they are so different in appearance from the resulting plant. I'm still on that learning curve.