Multiple private keys are more important than you might think, because Github won't let you use the same key in more than one account, so everyone who has more than one Github account and wants hardware tokens has to have multiple hardware tokens.
As you seem to use multiple GitHub accounts with SSH, you might be interested by the ssh_config tricks that I implemented in github-keygen
https://github.com/dolmen/github-keygen/
I didn't realize that, thanks for letting us know! We're actively working on this