All of the native Solid Tools convert components they modify into groups. It’s the way the extension was written. Some years ago at 3D Basecamp I met the author of those tools and when I asked about this he said to me, “They’re broken.” I hoped they’d get fixed but he had already retired by that time and evidently fixing them isn’t a high enough priority for anyone else.
Instead of using the native Solid Tools, use Eneroth Solid Tools and/or Bool Tools 2. Both of them respect the “component-ness” of components. I have both because sometimes it seems one works better than the other depending on the objects involved.