I have gone through and updated all existing EIPs to match this rule, including EIP-1.
In some cases, people were using markdown citations, I suspect because the long-form was a bit verbose to inline. Since the relative path is quite short, I moved these to inline but I wouldn't be opposed to putting them back to citation format if that is desired by the authors.
In doing the migration/cleanup, I found some EIP references to EIPs that don't actually exist. In these cases I tried to excise the reference from the EIP as best I could.
It is worth noting that the Readme actually already had this rule, it just wasn't expressed properly in EIP-1 and the "Citation Format" section of the readme I think caused people a bit of confusion (when citing externally, you should use the citation format).
Because Yellow Paper only describes the latest mainnet hard fork, there is not official source of information were the gas costs before the changes of EIP-150 are provided.