This using kubuntu 20.04 and a Gimp 2.10.25 appimage.
Deleting the user profile ~/.config/GIMP should have reset all the tools options.
However, the settings are held in ~/.config/GIMP/2.10/tool-options and a comparison between rectangular select with 'from center' and a default ellipse select is a single entry as screenshot, check what is there.
A couple of suggestions,
(1) Set Gimp up the way you want it start up, including un-ticking those expand from center options.
Then
Edit -> Preferences -> Tool Options
untick 'Save tool options on exit'
Click on 'Save Tool Options Now'
At the same time
Edit -> Preferences -> Input Devices
untick 'Save input device settings on exit'
Click on 'Save Input Device Settings Now'
Ok that and restart Gimp.
or...
(2) Go into ~/.config/GIMP/2.10/tool-options and delete the files
gimp-ellipse-select-tool
gimp-rec-select-tool
Otherwise as you say, a bit of a mystery.
Deleting the user profile ~/.config/GIMP should have reset all the tools options.
However, the settings are held in ~/.config/GIMP/2.10/tool-options and a comparison between rectangular select with 'from center' and a default ellipse select is a single entry as screenshot, check what is there.
A couple of suggestions,
(1) Set Gimp up the way you want it start up, including un-ticking those expand from center options.
Then
Edit -> Preferences -> Tool Options
untick 'Save tool options on exit'
Click on 'Save Tool Options Now'
At the same time
Edit -> Preferences -> Input Devices
untick 'Save input device settings on exit'
Click on 'Save Input Device Settings Now'
Ok that and restart Gimp.
or...
(2) Go into ~/.config/GIMP/2.10/tool-options and delete the files
gimp-ellipse-select-tool
gimp-rec-select-tool
Otherwise as you say, a bit of a mystery.