
The short answer is spPr is optional in the chart part, but its absence means “I have no formatting”. That’s why they are seeing this behavior.
More details:
spPr is optional, but if you remove the shape properties Excel will have to make some choices about how it displays things (colors are one of the things in that property bag). This element IS a part of the ISO standard though.
style1.xml and color1.xml for charts (a feature we call Chart Styles) are MSFT extensions to ISO 29500 and is not defined in the standards docs. They were added after standardization, in O14, and are documented in MS-ODRAWXML. One challenge is that because style information is stored in multiple places we have to determine which one is authoritative when they diverge. In those cases we sometimes will drop the chart styles from the file - which is completely fine because these are optional, nonstandard extensions.
By deleting the shape properties those now no longer match the style so we throw it all away to make it work. This is by design.
I also tested creating an xlsx file from scratch and you can create a valid xlsx file with a pie chart and the unique colors you assign in styles1 and colors1, and while Excel will open and render the pie chart and custom colors without the redundant spPr elements, the Excel the Chart Design tab will not work.