Trying to apply SP3 update on an existing 2010 SP2 server.

Setup prompts to /preparedomain even though it has already been done.

Went back tried to run all the various forms of preparedomain (preparealldomains, prepare specific domains etc.) and the issue still persists.

Double-checked all permissions (enterprise admin, etc.) 

Any idea what the issue could be?

Try to run the  SP3 from an elevated command prompt instead and see the results

Example:
C:\Temp\SP3>setup.com /m:upgrade /InstallWindowsComponents

Also check the exchange setup logs  and see the results

Tried - I've looked at the exchangesetup logs and there are no obvious errors or complications. At the end it just states 

[09/13/2015 04:47:37.0342] [1] [REQUIRED] The local domain needs to be prepared (via 'Setup /PrepareDomain') before server roles can be installed.