Yes, he can have two separate Schedule C businesses. They would need to be different types of work, such as you suggest, Religious and Education, since if they were the same, there would be no reason to have two.
Yes, the Religious Schedule C can list expenses only but be aware that a home office expense won't be allowed without income.
Even when the home office expense is allowed for both Schedule C's, you cannot claim the full amount of the home office for both businesses. So no, you would not claim 100% of the time for both businesses.
When the home office is entered, TurboTax does ask if the Home Office is shared. Be sure to respond "Yes" so the program allocates half to each (or whatever percentage you indicate).
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