(All this is purely IMO - I try to help the Yaru team out on an ad hoc basis but don’t speak for them.)
“bad feelings caused by modifying upstream icons”
IMO, because of what icons are, they’ll always have foreign elements from the desktop theme behind them.
Even when the desktop doesn’t use an organising device like blue tiles (Windows 10) or squircles (various iterations of Ubuntu), the icon will at least appear on top of the wallpaper. That has patterns and colours of its own.
Aside from personal taste, I’m not sure how putting an unaltered icon on a green or grey squircle is worse than putting it on a dark purple rectangle (i.e., directly on the Ubuntu launcher).
Actually redrawing icons to fit the aesthetic of a theme is a different matter, and I’ve experimented with that myself - at least once successfully (the maintainer of an app said we could do what we liked for Suru and actually liked our new icon).
But the blog post and tweet have called Yaru out for early experiments that put official upstream icons on top of coloured squircles. I’m surprised if that causes bad feelings because of the very nature of how icons work. They’re like stickers that get put on someone else’s desktop. They’ll appear with foreign elements behind them. The lawyer for another major app was perfectly happy for me to proceed with the mockup I sent, showing their (fully trademarked) icon on a Suru squircle. I guess they knew it would always appear on something that wasn’t part of their brand.
Also: not all icons are fully trademarked. It would be good if we could assume straight-talking when we read licences. They should be honest statements of what the creator is happy for people to do. If someone puts out a basket of apples with a sign saying, “Help yourself! Do what you want with these apples! You can even sell them if you like!” - it’s a bit unhelpful if there’s an extra layer of etiquette around what people should really do with the apples (especially when the farmer hasn’t complained yet, and it’s someone else feeling aggrieved on the farmer’s behalf).
Often, in the world of open source, the T&Cs are as liberal as that sign. When they are, it would be helpful if we could take it for granted that people would be fairly relaxed about a coloured shape behind the icon. But it seems we have to second-guess ourselves?
I’m happy to reach to developers and ask about icons. But, in cases where the licence says, "Help yourself! Do what you want!" then I almost feel a bit self-conscious, asking for permission to put the icon on a squircle. Example: in the video, the use of GIMP struck me as an odd choice, when the readme for that logo is so generous (“the use of Wilber.xcf.gz is free, though it would be kind of you to mention the original author… enjoy”).
Like I say, all IMO - but I think redrawing an icon and putting it as-in on a squircle are two very different propositions.