Not Updated For Current Season
The masteries shown here are not yet updated for the current season, the guide author needs to set up the new masteries. As such, they will be different than the masteries you see in-game.
Here's the build i use when I play mordekaiser.
I believe thatandis the way to go. Ignite is a must-have, since it spices up your ultimate nicely and makes it harder for champions to heal their way to survival. Ghost is a great escaping/chasing move, and lasts longer than flash for those marathon escapes all the way up a lane.
Magic penetration is one of the main focuses of this build, so these marks are very important indeed.
Pound for pound, these runes give you the best defense against auto-attackers out of any other rune. Your magic resistance will help you counter spells, and your newly acquired dodge chance will save you from DPSers far and wide.
These runes should be a staple to any character. Everybody from Annie to Warwick will hit you with spells, and this is your defense against them. This will enable you to shrug off nukes and allow you to focus less on defense and more on offense.
You are absolutely right, I said that health wasn't very important to Mordekaiser. And it isn't. Three of these runes will net you a bonus 100 health at the start of the game, and will also give you more room to cast your abilities, which all cost health.