"I wonder if and/or how much it matters if the bottom of the jack is above the red line as shown in this picture."
I don't quite understand. Is there a warning on the jack that says not to lift beyond a certain point? If so the purpose of that is to ensure that the jack doesn't loose stability when used as a jack. There is a point on a scissors jack where it is too tall relative to the width of the base to be stable.
Imagine the bottom edges of the base, measured along the longer side of the base, as the two bottom angles of a triangle. The top of the jack is the apex of that triangle. As the jack lifts, the base gets proportionately smaller, relative to the height of the jack.
In your use that shouldn't be too great a concern as the top of the jack will be attached to the frame.
Points to consider:
A trailer stabilizer is just that, a stabilizer. The suspension and the tongue jack support the weight
of the trailer. The stabilizers should prevent two things; up and down motion and side to side sway. Scissor jacks such as yours will provide the first, but not the second. They provide only a vertical moment only; a vertical post if you will.
If you take a look at stabilizers specifically designed for the purpose you will find that they deploy much the same as the outriggers on a back hoe or crane, providing vertical support and widening the trailers footprint somewhat.
It is often the case, and I speak from personal experience here, that it is better to go with the specific product for the job as opposed to adapting something because you found it cheap.
Myself, I would get a couple of the 650 lb Atwood type, that's 1200 lbs total, and use them in combination with the tongue jack to level and stabilize the trailer. Ask other Boler and 13 foot Scamp
owners on this site what they use. Then the recommendations will come from personal experience with trailers like yours.