You can increase the size of icons through Inkspace preferences. You can edit the menu entry to do that by default if it gives you desired result. I don't use Inkscape except for creating the odd text label but you can probably increase the size of the font in Inkscape by starting it with command GDK_DPI_SCALE=2 inkscape. Inkscape HiDPI support is work in progress I think, so it doesn't scale fonts for displays with very high resolutions (very small pixel size). I would suspect you have a HiDPI display because of that. Inkscape is a Gtk program so is a bit odd one out in this mix. Or the programs in question might not have support for HiDPI built in yet. Especially with things like fonts and HiDPI (if you have a display with very high resolution) the settings for your desktop environment might not be picked up by those kinds of programs.
You can run Qt programs on Gtk based desktop environments and vice versa and you should not normally spot that (it should look native) but there can be some papercuts when running programs developed with a different user interface library.
I don't have a solution but can say VirtualBox and Stacer are Qt programs.
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