Noticed this. When you say "fill-opacity is removed" is assume you mean set to 1.0, because new files still have it but set to 1.0.
No fill-opacity is the same as 1.0. New files have it set explicitly but it's a temporary workaround until I add fill-opacity slider to gradient and pattern tabs.
Also found something new from the gradiant color inherit. Everytime I click on solid color and back to gradiant it assigns a new linear gradiant. Do it a few time and have a bunch. Should it carry over but not add to the gradiant list?
Yes it's a known problem. Unused gradients should be removed automatically.
Where does it "say the correct size" and where do you read the selection size? Most likely these two readings use different length units.
Image Properties and the status line are correct.
They use SVG pixels, 1 SVG pixel = 0.8 pt
The selection width and height on the second button bar shows smaller.
This by default uses pt