The text might be meaning to place your keel flat on the grid, and then use the bottom of the keel as a baseline (see fig) to fix other heights, as well as lengths/radials etc. on the model. The bottom of the keel will always be accessible to measure from, and is a logical reference point. It is also worth noting with frames, that it is the outside dimensions that are important, the inside dimensions are often arbitrary.
Without seeing the book, I don't see a problem. In fact I can also see advantages.
Although the frames rest on top of the keel, they extend down the sides of the keel.
If you are constructing the hull upside down, you will still be able to see the lines marked on your keel when the frames are fixed down to a building board and the keel is bottom up.
My only question would be, 'is the bottom of the keel, shorter than the top of the keel?' Due to the stem end of the keel being curved. This would affect the measurements.
Usually, if I follow instructions, I find that things that seem strange in the instructions become obvious later in the build.
I am sure others will contribute additional helpful advice.