There are generally ways to compensate for resistant and/or immune enemies that you can stock - for example, there are cards that specifically go after undead. And remember, you can edit your equipment and deck mid-battle - you might have to skip a turn to reshuffle your deck to take advantage of the latter, but it might be worth it.
The trick, I think, is figuring out what your problem areas are going to be generally and finding those counters to them. I won’t claim to have mastered that art. And it’s gonna be much harder to manage in gauntlet modes where you don’t have a lot of room to go shop in towns or grind for reward cards.
Also, I think there’s some logic (not foolproof, but some) to enemy generation, at least in sandbox mode. Certain kinds of nodes and especially those destroyed towns or crypts or whatever that you can opt to go in will tend to have certain kinds of enemy. But I haven’t worked out exactly what it is yet.