Tomatilloes are strongly outbreeding, while tomatoes are strongly inbreeding. The consequence is that it will take a lot more time (and numbers of plants each year) to stabilize a new variety.
If the stature is genetic, you are still likely to not get all short plants next year from seed saved from shorty. However, every normal-sized plant will be a carrier for the short trait. Saving seeds from short plants each year will eventually filter out the tall trait.
In tomatoes, the dwarf and micro seedlings germinate a little bit slower than the normal sized plants. If you grow enough seedlings, you might notice the same pattern with your tomatilloes.
I say go for it. One of my projects is trying to stabilize a tomatillo line with inky-black fruit. Not sure how long it will take, but I've got the time.
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