Sorry in advance for the Wall of Text:
Completed a play-through in 8 hours and was able to discover that I had the chalice all along. Reading comments in here makes me wish I could help explain exactly what I did, but ultimately I don't know how to explain past make sure you explore. I found that there was never a "where do I go?" moment in the game for me and most information needed was marked with the floating ? bubble.
I'm fairly certain that you need to find every instance of the corpse digging for the Alma corpses (Vanae's minions give out info that you need), learn about the sacrifices below the church, enter the house in Saint Alma with the elders and get mistaken for someone else, learn about the chalice and how its a flawed creation (makes the holder greedy), read the book in the mages tower (especially to learn about revivification), talk to the sun king and kill the "failed" summon in dragon's den (this is so you understand why you have the chalice--the sun king talks about inanimate objects and how the soul infuses with it. The chalice --> alma, Gold --> the dragon), rescue Gee (you learn about how you were overthrown), and learn about Doris's past and almas quest for the chalice in the illusion town house (understanding why you revived in your body.
The mayor of the illusion town tells you about finding Alma which you find weird because shes dead. I believe it only tells you that something is amiss with the town, but I don't believe it causes you to realize anything about yourself, Alma, the chalice, or the ritual. I assume it's there for if you walk there before night hits, but it doesn't hurt to get the scene just in case.
The end game boss tells you what you already told Mary, so I'm assuming that talking to Mary is also potentially a requirement. One of the conversations I recall was that you desire the chalice so you can have an "infinite blood supply", which from the ending scene, I believe to be an important conversation.
I don't think the Kraken sidequest has any noticeable impact to getting the true ending, but that being said, getting the boat in the Elven Lands to get to the underwater temple requires you to see a scene about the end game boss remarking on the body of the Alma corpse there (part of the main story anyhow I believe). Unless its a required flag that the Kraken sidequest is completed, (turning the heart in to the guard for the gold reward) I doubt killing it is necessary.
I couldn't tell you if talking to Mary's father makes any difference outside of maybe a variation to the main ending.
I don't believe I missed any critical events during my play-through, and it was only toward the end that I started rushing slightly (skipping a couple chests, using invis to walk by enemies).
Only other thing I can think of is that nothing in The Phantom Castle itself makes any changes in regards to whether you get the true ending. Thus, when you enter the area for the first time could be a check of sorts whether you qualify for it or not. Totally conjecture but I'd suggest saving before even entering the area and double check all the other zones.
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On a different note, when I got to the second phase of the final boss fight, I had a 400 battle chain with Doris at lvl 30. Didn't ever need to sleep, and the amount of recovery resources you get during your travels is insane. Was a neat game, but I totally thought there was going to be a gallery unlock at the end based on the description--did not think I would need to still battle everyone.
TLDR: Trying to help and explain what I believe is required for the true ending, but I think it's mainly a matter of exploring everywhere. There could very well be something else important that I failed to mention -- I don't have any method of checking for more specifics without doing a new game+.