It’s certainly a hot discussion 
but I personally hope we can join the discussion and make some fair points to defend our preferred approach - even as we listen to reasonable points from other people.
One point I’d like to make is that, because of the very nature of how icons work, icon designers don’t control the pixels around their icons, or any that they make transparent. This is just a feature of what icons do. They’re like stickers that get stuck on someone else’s desktop. They can and will end up with anything behind them - even if it’s just the patterns and colours of the desktop wallpaper.
Here’s a non-Ubuntu example. As far as I can tell, in the case of Window 10, the desktop defaults to putting third party icons on blue tiles, because Windows 10 has a visual paradigm where icons are displayed on tiles.
Brand owners can certainly ship an icon for the Windows 10 style and control the tile colour. But, if they just ship an icon with an arbitrary shape and transparent background, I think I’m right in saying it will be put on a square and the square will be blue:
So for me, one part of the protest that I’d really like to challenge is the idea that brand owners wouldn’t be “happy” with their otherwise-unchanged icons being put on coloured squircles.
It’s a shame that an early test screenshot became a focal point for discussion about the script, because the colours were still a work in progress, and a couple hadn’t come out well IMO. But that’s an objection on the grounds of personal taste and aesthetics. If it’s wrong in principle to put an unaltered icon on a coloured squircle - no matter how good we make it look - then I think you could add the same “Would GIMP or Inkscape be happy with this?” caption to the Windows 10 screenshot above.
Also: even if an OS, desktop or theme doesn’t have a unifying device like buttons or tiles or whatever, there will still be the desktop wallpaper. Many OSes and desktops allow icons to be put on the desktop directly, and that means foreign colours and shapes appearing behind icons, and even showing through the transparent parts of them. The default wallpaper for an OS might be horrible for your icon. It might even be a grid of coloured squircles This is why I say that icon designers can’t control the surrounding pixels or ones they leave transparent. It’s just a feature of icons for them to be stuck on someone else’s desktop, which will have its own theme and visual paradigm.
The other point I’d like to make is that many users simply don’t like the approach where some icons conform to a shape and others don’t. OMG! Ubuntu! didn’t like it, and recently praised the new approach we’re developing. I think the Ubuntu French forum didn’t like the mix either, but I can’t find that post just now. Personally, I think the design of the Suru icons only worked in the original context of Unity 8 because the desktop itself added squircles to all third party icons.
If we’re going to continue using the Suru icons for “house apps”, I think we have to have to find a respectful way of displaying third party icons on squircles, analogous to the way that Windows 10 uses square tiles. In an ideal world, it would be something the launcher and shell do, which is how it works in Unity 8 and Windows 10 (because I very much doubt someone at Microsoft is adding blue squares in Inkscape, lol). But I think Ubuntu has to do it, or accept that Suru isn’t the right icon set for Ubuntu’s new Gnome desktop.
If, instead, we display the house apps as logos on squircle-shaped buttons, and gently encourage app maintainers to provide an icon in the same style - but only if they want - then the end result will always be a mix of uniform versus non-uniform icons, which too many users dislike. Sadly, I think the same is true if we reach out to maintainers one at a time and ask for permission to make a Suru icon on their behalf.
So: my favourite approach is for Ubuntu to have a shell and launcher that display non-squircle icons in front of a squircle, so third party icons can be completely unchanged but still look good next to Suru ones. My second favourite approach is to include a script that simulates this behaviour.
My third favourite approach is to manually simulate it for some of the most popular apps, again without actually changing the logo graphic at all. And my fourth favourite approach is to switch to a nice icon theme for the default apps that doesn’t use a uniform shape.
My least favourite approach is to use icons of uniform shape for the very small number of “house apps”, and simply hope that we can persuade app maintainers to accept or ship an icon in the same style.
Lastly, one point I hope we can agree on, among ourselves at least: Ubuntu, Yaru, and many Ubuntu users want a Linux ecosystem where distros (including Ubuntu) can have their own visual identity.
Some of the people participating in this debate don’t share that view and have come round to the idea that “themes” are not good. That’s a valid opinion that people hold for considered reasons, but it means we can’t expect everyone to see 100% eye-to-eye on Yaru, even if we find the area with the most common ground. In those cases, we won’t be able to convince everyone that Yaru’s approach is good, but I hope we can at least make the point that it’s permissible (in the spirit of open source, forking, etc.) and respectful to brand owners (comparable to how icons are treated in other OSes and in the spirit of how icons can be used cross-platform).