What presuppositions do you submit scientists make, and what presuppostions do you submit they should be replaced with?
The philosophies that the scientists adhere to color their analysis and make it impossible to be entirely objective.
Exactly what philosophies are those, and what exactly what philosophies should they be required to assume in order to insure that they are perfectly objective?
Nobody can be perfectly objective. Scientists would do well to acknowledge that instead of bragging about how they're trained in objectivity.
The philosophies guiding science have changed since Newton's day. He had no problem with establishing the scientific method while all the while believing in creation and that the Creator created an orderly universe capable of being systematically studied.
But to demand methodical naturalism as the baseline and insist that it is philosophically neutral is intellectually dishonest. Any presupposition of the supernatural by scientists is biased and a matter of preference because science can make no determination about the supernatural. So much for objectivity.