What are the key differences between the draft SHA-3 standard and the Keccak submission?
No they did not, the internals and security levels have not been changed from the draft Keccak submission, only the padding rule has changed.
The padding change is the only difference, this allows future tree hashing modes as well as the current SHAKE outputs to generate different digests given the same security parameters and message inputs. Up to 4 additional bits are added, which keeps the full padding inside a byte boundary, making implementations with octet only input able to switch to SHA-3 from Keccak with change to only a single line of code.
The padding change has no negative impact on the security of SHA-3.