Registry keys to change personalization settings?

Active Window Border

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Accent]
"AccentColorMenu"=dword:ffb16300

Active Window Title Bar

[HKEY_CURRENT_USER\Software\Microsoft\Windows\DWM]
"AccentColor"=dword:ffb16300

Inactive Window Title Bar

[HKEY_CURRENT_USER\Software\Microsoft\Windows\DWM]
"AccentColorInactive"=dword:ffb16300

Transparency effects

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Themes\Personalize]
"EnableTransparency"=dword:00000001

Show accent color on the following surfaces

Start, taskbar, and action center

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Themes\Personalize]
"ColorPrevalence"=dword:00000001

Title bars

[HKEY_CURRENT_USER\Software\Microsoft\Windows\DWM]
"ColorPrevalence"=dword:00000001

Default app mode

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Themes\Personalize]
"AppsUseLightTheme"=dword:00000001

Start Menu Tile

Haven't figured it out yet

App Accent Color

Haven't figured it out yet

Various Windows Explorer, and Taskbar settings

[HKEY_CURRENT_USER\Software\Microsoft\Windows\CurrentVersion\Explorer\Advanced]

For the answer above (Drew Chapin) - I suppose that's what you looking for:

Start Menu Tile and App Accent Color

HKEY_LOCAL_MACHINE\SOFTWARE\Microsoft\Windows\CurrentVersion\SystemProtectedUserData\S-1-5-******\AnyoneRead\Colors