1. The chosen number of 1000 games in principle is good enough for a reliable result considering that in most cases there will be an immense number of double opening lines. With narrow opening books (such as the strong books from
Stefan Zipproth one needs less games, 500, maybe even 250 games. With wide books perhaps more games are needed. Insider knowledge is required.
2. ProDeo isn't Stockfish, as one can see from the 3 matches ProDeo needs time to understand the moves the book is feeding the engine. Use at least a time control with one second calculation time, the more the better.
3. Testing different books, copy analyzed Polyglot books (with POLY) in book1/books and book2/books. Then open book.ini
[Book File = books\ProDeo.bin]
and change the bookname. Do this for book1/book.ini and book2/book.ini and double click start.bat.
4. The score margins 0.50 and 1.00 as mentioned at the beginning can be changed.
[Blunder Margin  = 100] * default is 100 centi pawns
[Blunder Margin  = 50] * default is 50 centi pawns
Also here insider knowledge is important. The ProDeo book is fully analyzed with Stockfish 12 and testing has showed that 100 and 50 are good settings. However a book analyzed with one of the latests Lc0 versions requires much lower settings because (current) Lc0 evaluations are much more conservative than Stockfish 12.