Epoxy to bond smooth aluminium to chipboard?

Glue doesn't work by "being absorbed into the wood" as you say. It forms a bond to the wood surface.

The problem here is your choice of material, chipboard. This s simply a compressed mass of wood chips held together with some glue. As you have discovered, those particles are not held together all that strongly.

It's not clear why you can't use some other means of fastening to this board but perhaps you might consider changing to something that has more going for it than chipboard.

If you must use the chipboard, you should consider using some thru-bolts with washers to spread out the load on the chipboard side. Alternatively some screws which are designed to hold well in such materials.

Particle Board Screws

You should be layering different viscosities of epoxy to do that job.

First, you should be "prepping" (sanding/wirewheeling) down the chip-board until you have purchase into good material.

For instance if you use Git-Rot, that is an epoxy which certainly does absorb into the wood (that's literally its job). Unmodified West System also will, but not nearly to the degree Git-Rot does. Or, one could use a 2-part epoxy primer, which when mixed and then reducer added to maximum spec, also soaks into the wood - you can tell because as you're painting the first coat, some wood areas will seem "dry" - the epoxy primer has soaked in. However this can only do so much: end of the day, chipboard is cheap, and simply may not have the strength you are demanding from it. Replace with marine plywood.

Once you have a reasonably stable, epoxy-drenched surface, now you can address attaching the aluminum. Glues don't like polished surfaces, so I'd give that aluminum a once-over with the jitterbug sander (noting that aluminum will gall up sandpaper, so this may be a challenge).

At this point you use an epoxy which is good at filling whatever spaces there are between. It sounds like the internal strength of the chipboard will be your limiting factor in any case, so adhesive filler vs fairing filler won't make much difference. I would mix the epoxy with fairing filler up to about a peanut butter consistency, or like Bondo... then apply that as needed to fill any voids. You don't want voids because that will concentrate the stress on the area of the chip-board that is in contact.