Couple of things to be aware of.
As you stated, make sure you do any renaming before you do your proxies. Renaming after the originals after the initial transcode session will be a disaster.
You could also create a folder structure based on the shoot dates, this way you aren’t interfering with any original metadata.
I’m not sure if you can rename the spanned C300 clips and get them to work properly. That would be a testing situation. C300 is pretty picky about its directory structure and index file, and as you’ve stated, Resolve doesn’t always play nice with spanned clips. I’ve had the same issue you are presented with …matching file names over different clips, but i’ve only created a new high res “master” file- say as a ProRes or something like that, renamed it, and then treated that ProRes as my camera original before transcoding. Again, not sure if you can rename some of those spanned clips properly, and keep the integrity of the folders.
Glenn