I hope that you learned that categorical factors may use either parameterization.
How do you think about the effects of the factors? The default Effect parameterization interprets the effects as a difference from the average response. So if Factor = level 1 has an effect of -10, it means that the response is 10 units below average. The hypothesis tests assume a null hypothesis of parameter equal to zero, or no effect or change from the average response. It is the default parameterization because that is how most people think about effects.
The GLM parameterization is a historical standard used by statisticians. It is the default in SAS PROC GLM. So it is included in JMP for comparison sake.