Well, first, on a light note, all of the action names are taken from Aerith in FFVII Remake, the closest White Mage to XIV's White Mage who actually does utilize nature in her gameplay. This includes Soul Drain, which is why I went with that name. That aside...
I respect the deep number crunching; however, one thing that I think is very important to keep in mind when we talk about theorycrafted ideas is that none of us have access to a prototyping build for the game. A handful of the issues you mention are things that are a result of lack of specificity, or things that could be easily caught during prototyping, like the issue of drifting. Another example would be you mention the rigidity of Soul Drain being a combo of sorts, but we never said casting a heal, or Dia, or Misery, or anything has to break that combo. Flexibility is important for healers, so anytime I think of ideas that work with procs or combos on healers, I default to the mentality that nothing breaks the combo except for simply timing out of it. And if we feel that the idea of it being a combo is still too restricting, then there are other simple solutions, like instead of a combo, it's a stack that you can spend of which you can stack multiple.
Ultimately, what I care about most is the idea, because if the concept is sound, then any knots in the structure would just be worked out if it were actually brought to testing. This is something that every job change has to go through anyway. Even a job that faces little change needs to be rigorously tested against the changes of those within the same role. And I don't want you or others to spend potentially hours trying to number crunch an idea of mine just to see if it works as it is written (unless of course you really want to I suppose). Cooldowns, stacks, numbers... all of these are very easy values to adjust and would be when pressure tested.
In other words, is the concept of building toward Tempest, Soul Drain, and Holy feel like a good idea, given that you can also have the option to have the process partially automated for those that maybe don't want to engage with it consciously.
Now, to talk about Afflatus Budding for a moment. One thing to note is that it was meant to have 2 charges, and it was meant to also nourish the Blood Lily since it's on the GCD and would ultimately increase the frequency of Afflatus Miseries. The other reason behind the idea was that it gives WHM total freedom to use their lilies on any GCD heal rather than feeling like Regen, Medica II, and Cure III are buttons you want to stay away from. That said, if it does feel like it's bottlenecking things too intensely, then we can simply cut that out and instead of the Holy trigger reducing the cooldown of that action, it just accelerates automatic lily generation by 5 seconds.
Another adjustment I mentioned in the past that I kind of just default to in my mind for WHM is that you should be able to generate 2 blood lilies, and just assign a cooldown of 20 seconds to Misery to prevent storing and dumping during buff windows. This would help with any issues of buff alignment on lilies because you can now more comfortably hold onto your blood lily for an upcoming buff window and not feel like you can't heal until after.
On the concerns for the Soul Drain MP generation feeling mandatory, a big part of MP management is because of a healer DPSing. If someone's not keeping up with their DPS, they're spending less MP. If that's taken into account with the values assigned to it vs what's gained through Lucid Dreaming or any other sources of MP management, such as Thin Air, then I don't think it's problematic. Instead, you can look at it as a way to manage the MP for someone that is maintaining their DPS. And for those that don't, it still allows them to have access to a very easy, "endless" source of MP at a loss, but anyone in that situation probably doesn't care about that loss anyway.