I suspect that having to "turn on" cloaking armor is due to game mechanics. If cloaking armor was always "on", you'd never be able to retrofit those ships, because cloaked ships don't show on the Retrofit/Scrap list.
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Cap'n Q
My first mod!
Hypermaze quadrant
The most merciful thing in the world, I think, is the inability of the
human mind to correlate all of its contents. We live on a placid
island of ignorance in the midst of black seas of infinity, and it was
not meant that we should go far. -- HP Lovecraft, "The Call of Cthulhu"