1. Since bottleneck just represents the "weakest" link in your environment, it is ok to have it on source side even if you're running direct SAN Mode. And yes, I would also expect the better performance rates for your backup job. Please review this topic for some tips and tricks that might help you.
2. No, we do not have any hard caps in the source code. Could you please tell me what Windows Server version do you have deployed on your proxy machine? If it is Windows Server 2008, then please take a look a this
post that might give you a couple of ideas on how to improve the backup job performance.
3. 100% of CPU utilization is not an issue, it is absolutely expected (for the on the fly data compression an deduplication) to have high CPU utilization during backup/replication job runs.