No, the result is not the same. When you look up the records for the <yourusername>.github.io you get a different set of records than the singular IP address they tell you to add if you want to use the apex domain!
So from Github's DDoS prevention's point of view, the result is different.
I believe the reason is that the *.github.io hosts point to a CDN rather than just having a single A record, and it is only when going through the CDN that you bypass the "neutering". Regarding your second question, it seems that github issues a warning if you do that:
So from Github's DDoS prevention's point of view, the result is different.