Ooh umm lots of Qs. Okay, well...
Just to clarify - it's a simple (very...) CLI c++ app that:
Checks the latest files.txt on the SoD server against the local files.txt
Files that have changed or been added are downloaded (ignoring the windows only files, sodpatcher.exe eqw.exe etc)
It then finishes...
Optionally, you can add a launchsod.sh script in the patch folder - the patcher will check for this files existence, and if it exists, will run the script once patching is finished. Otherwise, it simply finishes.
Therefore you could use the patcher 'manually' to download the latest changes when you know or suspect there's been a patch, or you can set it up (by making your own bash script) so that after you patch, or check for the need to patch, you launch SoD. Because you need to write the bash script yourself, it could be Cedega or Wine or whatever else you can get to run SoD. CPU binding issues would need to be dealt with in that script anyway so umm I guess you could say the patcher 'supports' it

Making a bash script to launch SoD with whatever command/variables/etc you like is flexible and very easy.
If you have access to run SoD you presumably have RW access to the E-Q folders anyway - so all access issues are ignored - also simplest/laziest option.
As I said, it's very simple - I kinda chose that a)inadvertently, I'm lazy... and b)because many people will have varying setups (cedega/wine etc minimum) and simplicity, hopefully, ensures wider support for varying setups.
Having said that, I've only tried and tested it myself, so I've really no idea how it will work for other people - I see no reason for it not to work fine though.
It's very basic and only the first version - idk if there'll be others, - there's certainly plenty of things that could be added to make it 'friendlier' (gui, error checking for inet connection, etc)