OK, one thing that works is to build libLerc
https://github.com/Esri/lerc/tree/master
(which is the one throwing the error) manually and link the official msys libstdc++ statically to it and ship this library in the Geany installer instead of the msys one. I tried this manually without modifying the build scripts and Geany launches. So if there's not a better way, this could be one way forward.
Just to clarify my confusion: using the original libstdc++ (https://github.com/geany/geany/commit/110c7b492e8595851131eeb5c381418799e8ae...) the Lerc error still persisted? Even if and the rest still works, I'm happy to remove this hack. Maybe the toolchain changed since I added it a year ago.
I'm wondering why I don't see these errors, I think the only difference is that I'm on oldish Windows 7.
Regarding librsvg: I see the red boxes as well, not sure why. librsvg is included and at least its direct dependencies as well. I'll try to have a deeper look but this might take some days.