The problem is that your vet doesn't understand the proper application of ivermectin or how it works, and doesn't understand rabbits. Which I don't quite understand since you are in the US right. So your vet should have some understanding of how ivermectin is used and should be able to get a hold of the right kind.
Dosage is important. Too high of a dose of ivermectin will cause overdose symptoms, too low won't get rid of the mites and can lead to resistance. For your vet to just have you apply a 'small amount' is not an accurate way of dosing, so you don't really know if the proper amount is being applied.
Next is your vets dosing frequency. Ivermectin should be applied or given for 2-3 treatments 10-14 days apart, to get the next round of eggs as they hatch and before they mature. So that also means you would
not be washing your rabbit to 'get rid of the eggs', which is frankly a ridiculous thing for any vet to be suggesting, as first it won't get rid of the eggs unless using a specific shampoo(which in most cases you shouldn't be using on rabbits as it may not be safe), and second you shouldn't be bathing a rabbit at all unless an absolute necessity, which this isn't the correct circumstance.
Then there's applying a cream to a rabbits skin is messy and a pain in the butt, which no experienced rabbit vet would suggest for this kind of situation. I would never want to apply a cream unless first I knew it was safe if my rabbit groomed any of it off, and if there was only bald skin to apply it to with little or no fur in the way.
Because it doesn't list the inactive ingredients, there's no way of knowing if it's safe for him to lick it off. If you've already applied the cream and it's to your rabbits back near the nape of the neck, your bun shouldn't be able to reach back there to groom it off. Which would mean that it would be safe to not use the cone. If it's lower down and your bun can get to it, you may have to use the cone and monitor your bun closely. Or I would consider wiping it all off as much as possible and starting treatment over in a week, but putting the cream at the nape of the neck where it can't be groomed off.
Cones are difficult to use with rabbits because it can make them depressed and cause reduced eating, which can then lead to gi stasis setting in. So the rabbit has to be closely monitored to make sure it's eating and drinking well throughout the day and night, and it also needs to be able to get to it's cecotropes to ingest them, which a cone makes difficult.
But you also have to consider if your bun is getting the correct dose. The dose of ivermectin for rabbits is 0.4mg per kg of body weight. If there is 4mg per gram of the cream you are using(which needs to be verified), then that would mean there is 0.4mg per 100mg of cream. For a 3.6kg rabbit, that's 360mg of cream applied to get the 0.4mg/kg dose. I suppose you could just apply the 'small amount' that the vet suggested and hope it's the correct dose to get rid of the mites.
Another option is if you can get a hold of injectable ivermectin or get some from your vet, I would be inclined to start treatment over using that. What that would entail is cleaning off the cream as much as is possible, wait a week in case any was absorbed, then I would measure out the correct dose of injectable ivermetin but give it orally with an oral 1cc syringe. A 3.6kg rabbit would need 1,4mg of ivermectin. The injectable solution here in the US is 10mg per ml(1% solution, which needs to be verified), or 1mg of ivermectin per 0.1(one tenth) of solution, which would be 0.14ml dose. It's basically just a drop or two. The other option is if you can get Revolution/Stronghold(selamectin). That is a topical application to the nape of the neck that only has to be applied once at a dose of 18mg/kg. So these are just things I would consider doing if I wasn't comfortable using or trying the cream. But you do have to be comfortable measuring out doses as an overdose of ivermectin is dangerous.
http://www.medirabbit.com/EN/Skin_diseases/Parasitic/furmite/fur_mite.htm
http://medirabbit.com/EN/Skin_diseases/Parasitic/earmite/Psoroptes.htm (for selamectin dosing)
If you are going to stick with the cream, I would apply the cream to the nape of the neck where rabbits can't reach back to clean it off, in 10-14 days, then again for a third treatment another 10-14 days after that, for a total of 3 treatments. With
no bathing of the rabbit. If your rabbit is getting the correct dose of ivermectin then this should clear up the mites entirely.
I'm not a vet, but these are just things I would consider and might try in a similar circumstance.
