Sigil creates a file user_prefs.json in path C:\Users\<USER>\AppData\Roaming\sigil-ebook\sigil\QtWebEngine\Preview\ on every run.
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I can confirm this is an issue. If you open up the SigilPortable.ini file within SigilPortable\App\AppInfo\Launcher, adjust the DirectoriesMove entry as follows:
This should handle portablizing the additional settings.
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This is fixed in Sigil Portable 2.0.2 Rev 2.
Sometimes, the impossible can become possible, if you're awesome!