Wow some people can be ignorant pricks!!!.

Should I feed my snake/lizard/gecko in a separate container?

No. Nope. Nyet. Good grief, NO.

There are some pieces of "advice" that continually float around, and never go away. They are constantly recycled, often regurgitated without actual thought to new keepers struggling to separate good advice from bad.
There is no sensible or logical reason to feed your reptile in a separate container. The most common reasoning is that it "trains" the animal not to bite when you go in the cage.

There are two basic reasons your animal strikes when you go in the cage. Most likely it is a defensive strike, as you have startled the animal (perhaps woken it up), and it is defending itself. Learn how to approach your animal better, don’t grab it by the head, or from in front of the nose. "Wake it up" before snatching it out.

The other common strike is due to the fact that you SMELL LIKE FOOD. Don’t wear "rat cologne" and don’t feed by hand. Use a hemostat for goodness sakes! Again, this is not the fault of the animal, this is due to the ignorance of the keeper, and it is easily remedied.

Feeding in a separate container does not "train" the animal to be tamer when you go in the cage (you still "go in the cage" to inititiate feeding). And in itself it does not prevent impactions of particulate substrates like soil or mulch.

You know what DOES prevent impactions? Proper husbandry! We have kept thousands of reptiles, snakes and lizards, on MANY different substrates, and feeding doesn’t cause impactions. Bad choices do.
Impactions are most often caused by low hydration levels. When an animal is dehydrated, nothing is going flow as smoothly as it should. When an animal is kept too cool, metabolism is not going to run well enough to pass substrates and other non-digestibles.

I suppose if you kept your gecko on a substrate of crushed glass, then any glass consumed while feeding would cause a problem. But that is because you chose CRUSHED GLASS (or walnut shells, or some other poor substrate). Pick an appropriate substrate. Don’t chronically dehydrate your animals (a SUPER common problem and misunderstanding in reptile husbandry) and give your animals the necessary range of temperatures to accomplish life events (like pooping!).

And stop feeding in a separate container. That is just dopey.