In the photo you posted, everything in the bilge is wood covered by fiberglass. The hull is cored with balsa wood and the the stringers or floor timbers are wood and covered with fiberglass. Penetrating the skins on these parts would put the wood at risk of getting wet.
When you talk about the engine bay, I'm not sure which parts of it you are describing. The two longitudinal ribs that the engine sits on are most likely wood encapsulated with fiberglass.
Epoxy is very brittle, it needs fiberglass or some other thickener to make it less brittle. Thickened West System epoxy or Jamestown Distributor's Total Boat epoxy would be good choices. Both West (SixTen) and Total Boat (Thixio) make epoxy in easy to apply cartridges this would be appropriate for this application.
To
@thinwater's point about wood in the bilge being a bad idea, in general he is correct and I would agree with him. However, in this case it is not a critical or structural application, so I would be less concerned about the wood. If the wood should rot, then just grind it out and put in a new piece. If you can use a rot resistant wood like white oak this would be less of an issue.
A Weldmount stud would be the most durable and most expensive option. A piece of pine glued to the side of the bilge with HW store epoxy the least durable and cheapest option. Drilling and screwing directly into the hull the worst option and one the should be avoided at all costs.