When themes are made the initial icon placement is determined by the theme author, or by a standard default if they don't specify placements. There really is no way to make a theme and have it use the icon placements that you've made on a totally different theme.
I do understand and sympathize with you tho, that bothered me too when I first set up the default Precision theme and then switched to the Silver theme and everything was out of order. That's when I realized that I would have to customize every theme I tried or used, but at least it only had to be done once.
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