My advice, same as anything, do not be too ambitious initially, get one thing working and work your way up.
I have not even looked at Inkscape themes before your post
I can get using Inkscape 1 (appimage, kubuntu 18.04)
1) A stock theme look like this: Not keen on two of the defined colours, and one of the icons
https://i.imgur.com/Ne8okxm.jpg
2) Edited the highlights.css file as Inkscape doc. Found the pointer icon (tool-pointer-symbolic.svg) and edited that.
https://i.imgur.com/YFG0p6s.jpg
The usual precautions. You should be editing the files in the Inkscape profile
~/.config/Inkscape/icons/renamed-new-theme/ so even when screwed up no real damage done.
Even then, not a bad idea to copy an icon file to another folder and rename the original as a backup (something.svg.bak)
3) With the new icon in place and the new theme selected.
https://i.imgur.com/RQUm5CD.jpg So it is possible, new icon and using the colours specified.
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My guess. The icon svg files are not quite the same as your
made-from-scratch.svg icon. As far as I can see you are stuck with the 4 defined colours. The svg has a section for that. Still using the Inkscape defaults, presumably the use highlights.css overrides.
https://i.imgur.com/XSg3NPS.jpg
What I would try first. Get one of the existing icons, copy paste your new icon into it and check/hope the original icon properties remain when it is saved.
