How do you configure the Transaction time out in Entity Framework 6 DbContext.Database.BeginTransaction?

If for whatever reason you need to manage transactions yourself it is much easier to use TransactionScope. It has several constructors accepting a TimeSpan parameter to set the timeout. For instance

using(var ts = new TransactionScope(TransactionScopeOption.Required,
                                    TimeSpan.FromMinutes(1)))
{
    using(var ctx = new MyContext())
    {
        // Do stuff.
    }
    ts.Complete(); // Try - catch to catch TimeoutException
}

I'm curious though why you want to set transaction timeout, not command timeout.