The terms "Total Flour" and "Total Dough" were both used appropriately and not inconsistently. As I said, the preferment % is usually measured as a % of the Total Flour.
The tool allows for either (and also as a % of Total Water). The particular recipe you are asking about is looking for it as a % of Total Flour. You are right, it does not specify and he is not super clear about which he means.
But, it really does not matter much or at all in this case (and in most cases where the preferment % is relatively low). This is even more so since he is actually specifying the number of grams for each ingredient and you can just scale.
The flour at the top, which is without the preferment, is 456 grams and the preferment is 37. So, 37/456 = .081 (so, to the nearest %, it is 8%). On the other hand, the Total Flour is "really" 456 + 37/2 = 474.5. And, the flour in the preferment is 37/2 = 18.5. The ratio is then 37/474.5 = .078 (so, to the nearest %, it is 8%).
On your second item, being to omit the IDY - Craig has made that point (trust your starter, no need for IDY to "help") in many places, many times. But, it is always a companion point to his point that he avoids cold fermentation. He is a strong advocate of room temperature fermentation, especially with sourdough starter. You will not find him saying you will be successful with a cold fermentation of dough with sourdough starter.
So, please watch out for context.
In other words, if you omit the IDY and only use sourdough starter, then don't cold ferment the dough. Many have tried (including me) and all or most do not get a good result.
The Pizza Raquel recipe calls for cold fermentation. So, if you do not cold ferment and you are changing the sourdough/IDY specifications, you are changing the recipe in a very significant way.