I doubt installing OwnCloud from their sources will 'break' anything...., but then, you've just touched on one of the advantages to buying it in the Marketplace...a lot of work/time has been spent making sure the installation on ClearOS goes smoothly and is automated to every extend possible. Hence, the convenience of essentially 'one clicking' to install via Marketplace. The other value add is the tight integration with ClearOS directory API.
I've had issues with this, but completely unrelated (I think) to file permissions) and something to do with naming conventions. I've been too lazy to follow this document (specific to TV shows) but have always assumed that because I've ignored it, I'm going to run into issues.