Here's an idea to utilize DoL and DoH classes in instances:

Miner:
Plant explosives to blow up road obstructions
Collapse tunnels to prevent being overwhelmed
Break pillars to crush bosses

Botany:
Cut vines to make ropes (+weaver) to climb up/down cliffs
Cut down trees to ford a fast flowing stream (+carpenter)
Make traps to bind, slow, disable enemies
Cut down trees to prevent flying creatures from resting in the branches

Fishing:
Allowed to throw spears (spear fishing) to disable fish-like monsters
Hold monsters down by netting them
Fish up secret weapons from pools (e.g. a specially virulent toad to make poison, +alchemy)

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Interaction can be simple, like harvesting points - Perhaps a different mini-game to spice things up.
Make things exciting - Spawn mobs to attack when the DoL or DoH is working.

For initial instances, make the requirements low, like R10 or R20 so that people can slowly accept this type of instances. Make it completable without actually utilizing the classes but apply penalties or bonuses for the lack thereof or presence of them.
E.g. Break a pillar with your weapon but suffer 50% durability loss.