A few things I noticed with .bbColorSchemes:
1. The plist accepts different color specifications
You can use RGBA:
<key>BackgroundColor</key>
<string>rgba(0.979995,0.979995,0.979995,1.0)</string>
or HSLA:
<key>InsertionPointLineHighlightColor</key>
<string>hsla(0.760, 0.310, 1.000, 1.000)</string>
or web colors #RRGGBB:
<key>InvisibleSpacesColor</key>
<string>#F08080</string>
and maybe some more.
Apparently you can use any combination of the above in the .bbColorScheme plist and BBEdit will recognize the color.
2. If you edit a color in BBEdit's color picker, the color will be saved in HSLA in the .bbColorScheme.
So if you pick a RGBA color and BBEdit saves it in HSLA, some conversion must occur that might explain the difference of colors between the chosen color and the displayed color. It could be float truncation or color space conversion depending on which color profile is in use.
3. This interesting video shows some little known features of the color picker, notably the presence of the color profiles and some more.
HTH,
Jean Jourdain