I was also confused about this so I want to put it in numbers so that it makes sense. I have a Bloodcrag Minotaur in play with 14 Max Life and no damage on him. Mort attacks my Minotaur and does 2 damage from his attack and then rolls for effect and is successful in placing a tainted marker on my Minotaur. After the action phase is complete, my Minotaur has 9 of 14 life? 9 of 11 life? or 11 of 11 life?
The way I had initially read the rule, I would have said 11 of 11 life because the 2 damage from the attack would have brought the Minotaurs health down to 12 of 14. Then the tainted condition would have lowered his max life by 3 to 11 therefore giving him 11 out of 11 doing 1 extra damage by lowering his max life. The reason I interpreted it this way was because the codex says it deals 3 damage and that this damage cannot be healed, but that the tainted marker does not count as damage dealt by the attack. Since the damage dealt by the tainted condition is not dealt by the attack, I assumed it meant it was an attack on max life as it is unable to be healed. It also seemed strange that the damage that is unable to be healed fell in the middle of the creatures Life amount. For example, let's say the tainted damage brought the Minotaur from 7 of 14 down to 4 of 14, I could not heal damage 5, 6 and 7 but could heal 8-14. Since the game is intuitive, and this idea seems ridiculous, I again assumed it damaged max life.
However, based on what is spelled out above I would say he has 9 of 11 life (11 life now since 3 of the damage is unable to be healed) and that the tainted marker acts as both 3 extra points of damage during the effect and condition step AND minus 3 from max life since it cannot be healed. The 9 of 14 option seems least likely since the tainted condition does damage that cannot be healed unless the marker is removed, so the Minotaur cannot have 14 life while inflicted.
Thanks for reading my post and I apologize for the long-winded question, but I really enjoy this game and want to ensure that I am following the intent of how the game was designed.