So I create a new page in Sparkle, set the background color to #123456, then check it with Apple’s Digital Color meter, and it has a different value. Is this is some kind of color space issue?
It certainly is a colorspace issue. Perhaps Sparkle could work better than it does in regards to color space management, but frankly it’s not obvious how we should change it exactly.
Yes, I don’t think there is a way to fix this via Sparkle without breaking something else.
If anyone else runs into this issue, it seems that the Digital Color Meter reports values after OS X adjusts them for the color space selected in system settings for the monitor. If you change the monitor’s settings to “Display,” the Color Meter will report the correct values.
Also, it seems that the system eye dropper tool (accessible from Sparkle via the color well) somehow compensates for the current color profile, so stick to that and everything should be correct.