I think the first step in fixing this is to disable HALPMEH from casting when you don't need it, i.e., when your HP is full and you're not poisoned. I beat Indomitable using a Gnome Wizard casting BICEPS and GETINDARE, which worked but wasn't a cakewalk since those two glyphs can't be recast until they wear off (upon attacking, and thus receiving damage, and thus needing to regenerate and to let the monster regenerate if you're trying to avoid leveling up).
The second issue I see is that Gnomes are overpowered. Relative to the other mana-heavy race, Elves, they are nearly double as effective as they were in the alpha (Elves get less of a boost, Gnomes get more). Mana potions are incredibly valuable, and Gnomes also don't have to worry about conversion until the last minute since they get the full benefit whether they convert right away or wait until the boss (most other races see an immediate benefit to conversion, so waiting longer than necessary to convert means you are wasting resources). I would suggest raising Gnomes back to the full 100 points for a conversion bonus, maybe even increasing it to 110. (I think Halflings are probably fine at 80, at least for now, symmetry be damned.)
Regarding Mysteria herself, I'm not sure that she'd be all that unbalanced if HALPMEH could no longer be spammed. However, it will still be easy enough to get very high max MP and then have her remove all the magic resist that she gave as the side effect to the boon, and still way too easy to ignore the magic resist altogether if you're not relying on fireballs, which is much easier than in the alpha now that Mysteria no longer hates physical attacks. Maybe her Magic boon should give monsters physical resistance? 1% to magic and 1% to phys, but she'll only ever remove the magic resist seems both fair and fitting to her personality.