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.
Why don't you just try it like Nick said and plug your ClearOS Eth1 nic into a LAN port on your DD-WRT router and keep the DHCP server disabled on your router since you're using the ClearOS DHCP server; especially this since you want to use the content filter. Connect the ethernet switch/HUB you're using in the house to another LAN port on your DD-WRT router. Keep your proxy and content filter servers running with the proxy set up as transparent. I have never had a problem where the content filter gets bypassed when using this configuration. Connected like this you can either use the DD-WRT router as a Wifi access point, or the HUB if it's something like a Unifi access point. You wouldn't have to dink around with any settings in the router after this, especially since you're using ClearOS as your gateway and it does all the work. Sounds like that's why you implemented it in the first place.