You absolutely raised some valid concerns. And I hope, I hope, I hope that startups aren't using these templates as-is (or possibly at all). Each company's business operations, policies, risk tolerance, etc. will be different and their standard contracts need to reflect those positions. They need to have lawyers write the agreements/policies/etc. to make sure they're following all applicable laws.
However, I think that Ironclad (and possibly others) are trying to make the administration of those contracts easier. Real trouble, from a business perspective, comes when the company gets bigger and they don't know the risk on their books because they can't manage their contracts.
I don't think these tools will cut out the lawyers, but instead help the companies manage their contracts and be able to better use us lawyers.