Simple example: SVG pattern striped.svg

Yes.

So the fix was adapting a find in jQuery, after the HTML had been changed. Could someone also link that HTML change? I suppose there must be some protocol to check depending JS before changing the HTML. It would be useful to figure out what went wrong.

This file seems to show the problem: SVG text positioning.svg

This can probably be closed. I just realized, that my browsers show some thumbnails with wrong colors.
Maybe I was wrong about this in February. Or maybe the problem existed then, and was fixed with the mentioned update.

This also affects shades of red. Here is an example where pale #eb4e4e is rendered as bright #ff1d3e:
https://commons.wikimedia.org/wiki/File:Family_1110_1111_1110_1010_(Zhe_8329).svg

In T329336#8826122, @hnowlan wrote:

Is this issue still present? After version upgrades it appears to me that thumbs now match the original colours

Not just PNG and SVG, also JPG.
https://commons.wikimedia.org/wiki/File:BlueCyanGreen_PNG_screenshot.png
https://commons.wikimedia.org/wiki/File:BlueCyanGreen.jpg
From the following file I get the impression, that the problem is negligible for TIF files:
https://commons.wikimedia.org/wiki/File:IUSM_logo-2.tif

extract the PNG and overwrite the SVG with the extracted PNG, so that in the file-history is a mixture of file-types

Yes. That is the first use case I described.

See my answer at Commons talk:Overwriting existing files.
The community has no interest to extract wrapped raster graphics into separate files. That makes sense, because duplicates are annoying.
My request is to make it possible to overwrite wrapper files with the extracted file.