I haven't noticed that! I admittedly use preset embark profiles most of the time, so I haven't seen it happen. And I'm not sure what to do about it either, as making them as cheap as anything else or removing them from the civs availabiliyy lists aren't really desirable options. I have also noticed, with a completely different mod, that I've somehow got them embarking with 50k points even though that shouldn't be possible. I brought cave dragons on embark. No idea how, either.
The fire thing, yeah, usually not a good idea to let the general populace have access to fire magic. I learned that like 8 years ago when I made cows breathe dragonfire on a whim; everybody died when the goblins attacked. Again, short of removing those effects there's not an easy solution. I would suggest keeping the magic workshops and their products separate from the rest of the fort both by distance and by burrow/stockpile restrictions, as usual. Only allow safe, non-fire-starting essences into the general dwarf/kitchen stockpiles.
You can also intentionally cheese it by incorporating spell essences into large stacks of prepared meals for the population to consume. For instance, I took a cheese elephant that came from an elven caravan and butchered it for a stack of 401 cheese, bought three stacks of 5 each essences of recuperation, shielding and holy spike, made a roast of all four stacks, which provides 416 servings providing all three magic effects to anyone who eats one. At least I'm pretty sure that'll work. The ones who ate them so far haven't been involved in combat yet so they haven't used their abilities, but I'm hopeful!
In development news, I've squished a couple bugs, renamed mammaroths to giant mammoths (I think there's only a couple mods that use mammoths at all anyway, so It probably won't get confusing) there's new summoning effects for any creature and any demon, dwarves will hopefully cast the spell to summon the critter pretty soon after eating the essence.
Summuning demons summons any creature with the [demon] tag, so it will summon the procedural demons from worldgen or the ones I or other modders have written. Procedural demons would almost certainly destroy your fort if they get summoned in an area that isn't secured with legendary warriors to fight them.
Summoning any misc creature will summon any valid creature at random, the only things that are off the table are vermin and a couple instances that might crash the game. So you could end up with a demon, a megabeast, a titan, a night creature, a human, or a deer. Anything.
Don't let random dwarves eat these, either. Probably shouldn't even make them without a secure facility to quarantine anything game-ending.
Using the tome of planes tool I'm going to let you narrow it down to more specific creatures or products. Working on that right now. You can still acquire one through trading via the "exchange" reaction in the conjuration circle.