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These days they're very similar - In the past ProAuto has been considered more lax in how the operation runs, but that's really not the case - both run tight ships, and safe DE programs. The racing programs are a bit different but I enjoy both.
Pro's DE program is a little more laid back. If it's your first time at Pro they will make you do the new member class for a day for insurance reasons. No mandatory downloads, etc. Just run safe and have a good time.