Well if you had not done any grouping, it's possible the draw.io program did it. But if you had inadvertently double-clicked on the group (which enters the group), then saved the file that way, the file might have ended up that way I saw it. (emphasis on "might")
I can't open that draw.io file. But if you can attach the SVG file which it produces, without doing anything to it, that would at least give me a hint that the problem comes from draw.io.
Ok, never mind. I searched it out, made a simple drawing in Draw.io, and exported an SVG file. It does not show this problem. It shows a proper group, not an entered group. So I can't reproduce that problem. Maybe when you edited the file in a text editor, it changed something?
You say you edited the namespace? Geez, I can see why wikimedia rejected it. That code is totally borked! I'm surprised Inkscape can open it at all. The entire code from svg to /svg, is on one line. Tags are missing. Maybe the problem does come from draw.io, but I would need to be able to reproduce it, before I take the step to post a warning about it.
I can't seem to reproduce this in Inkscape, that having entered a group and then saving the file, it opens as being already inside the group. If we could figure out how that happened, we might report it as an Inkscape bug. I've been trying to make it happen, but so far, I can't. I did see another person with this problem (maybe a couple of years ago), so I think there could be some way to do it. But so far, I can't figure it out.