Firstly, thank you for tackling this regression.
installed and now testing …
My my CSS file and CSS note
(1) /home/todd/joplin-css-test.css:
p { color: green !important; }
(2) resource cd684768653248e09c681b2d85b247cb:
<style>
p { color: green !important; }
</style>
CORRECTION: that resource did not have the <style></style> elements. Since, I treated it like a CSS file. And so, I was just the same as the on-disk joplin-css-test.css file:
p { color: green !important; }
Test Notes
My test note v1:
<style>
p { color: green; }
</style>
This should be green.
Result: the text color is indeed green. No errors in the console. But all notes turn green (even if they don't call the CSS).
The CSS should be flushed every time you move off of the note (or change the note at all). And it should never apply to any other note. Heh.

My test note v2:
<style>
@import ":/cd684768653248e09c681b2d85b247cb";
</style>
This should be green.
Result: the text color is indeed green. No errors in the console. All notes turn green (even if they don't call the CSS). 
My test note v3:
<style>
@import "/home/todd/joplin-css-test.css";
</style>
This should be green.
Result: the text color is indeed green. No errors in the console. All notes turn green (even if they don't call the CSS). 
My test note v4:
<style>
@import "file:///home/todd/joplin-css-test.css";
</style>
This should be green.
Result: the text color is indeed green. There IS an error in the console. And again, all notes turn green (even if they don't call the CSS). 
Not allowed to load local resource: file:///home/todd/joplin-css-test.css