The auto-minimizing would introduce a new problem - what if you want to pick a color from Rapid PHP window (e.g. Preview tab)?
After some time of using Rapid PHP now, I found those "preview" panel not very useful, at least _for me_ it's useless. Besides that they don't really work (maybe I just misconfigured it), I want to preview my websites on a "real" browser in real size. So Alt-Tab between the IDE and the browser is practically constant.

But to solve your argumented problem, I would set a checkbox in the options to tell if Rapid PHP should minimize itself when color picking. So everyone can choose what he wants.
As a workaround you can avoid maximizing Rapid PHP window before picking the color and put the webpage you want to pick from next to Rapid PHP and make sure it's not covered.
OK, since I work only in fullscreen and with dual monitors, I didn't thought of this possibility. Also, the fact that the colorpicker isn't available on the second monitor (it seems it only works on the primary monitor) supported this ignorance. And honestly, I really would not think about "windowing" and positioning Rapid PHP every time I want to pick a color.

So, in this case of your suggested workaround, half of the way would be already accomplished. Building an selectable option for automated minimizing (for those who want it

) would be the other half.
Maybe this option finds it's way into Rapid PHP.